GreginDenver

Good job being thorough, doing all the related hoses and O-rings. In case you ever need to remove the throttle body assembly again, an easier/gentler method is the "cargo strap" approach. First use a hair dryer or heat gun (on low heat) to warm up the boots and make them more pliable, then loop the cargo strap through the rear corner of the throttle body and loop it over your own shoulders/back, then use your hands on the frame rails for direct upward leverage. This way you can be gentle and firm at the same time.

This! ^^^^^^^^^^^^^^ (I should have mentioned this in my first post). Because the VFR800's thermostat is buried deep down in the "V" of the engine it's a difficult item to remove and replace. This problematic location causes a lot of VFR owners to defer any maintenance on it, and now the 5th Gen VFRs are over 20 years old. I own two 5th Gen VFR800s, a '99 and an '01. I replaced the thermostat on both bikes right after I purchased them because on both bikes the thermostat was original, which means they were 20 years old. In the time I've been paying attention to 5th Gen VFRs (and occasionally purchasing them) I've read about a lot of cooling issues. It appears that a 5th Gen thermostat can fail in the fully-closed position, fail in the fully-open position, and the thermostat can also fail in a way that results in a reduced range-of-motion (never going fully-closed or fully-open). If this new-to-you VFR is running on the hot side there's a good chance the 20-year-old thermostat isn't moving like it used to. And your prior owner was "slapping bandaids" on the situation with his ridiculous radiator fan switch.

Sounds like you're in for an interesting time with this new-to-you 5th Gen. Obviously the prior owner was fighting cooling issues (or he thought he was). I would carefully go over the bike to insure that all of the OEM heat-handling items are in place (such as the rubber flaps over the front and rear cylinder heads).

Seeing that your VFR is a 6th Generation bike makes me wonder if your tachometer problem might be due to Grounding (rather than Power). It is a known fact that the 6th Generation VFRs have a Multi-Connector Plug that can cause weak path-to-ground problems with everything and anything on the front of the bike. If I remember correctly this is the infamous "Blue Connector" problem. I'm not a 6th Gen owner, so there are probably others here on the forum who could give better/more accurate advice on how to determine if your VFR is having grounding problems due to "Blue Connector" issue.

Yeah, once the shaft-seal starts to "weep" it isn't going to stop, it's only going to slowly increase, and if your brain is anything like mine you won't be able to ignore the leak well enough to enjoy riding any more. Here's what my '99 looked like for a while. It made me miserable until I replaced the water pump.

I always find that pictures help me to understand. This image is a screen-shot captured from the digital version of the 1998-2001 Honda VFR800FI Interceptor Service Manual, Chapter 13, Page 15. I'm guessing that this checking of clearance (and, obviously, re-adjusting the front wheel axle placement if necessary) to get 0.7mm on both sides has the effect of optimizing the spacing for the brake return-slide action.

It sounds like you're saying: While your hand is releasing the clutch in a normal, progressive manner, the resulting "action" of clutch engagement that you're experiencing seems to have something like a sticking-point or hesitation in it, meaning that the clutch movement isn't exactly following the command that your left hand is giving it (something is causing the Clutch Slave Cylinder to "pause" or momentarily stick in place, causing a noticeable slow down as it transits its range of motion during your clutch-lever release). If this is the case I'd say it sounds like the rubber sliding seal inside your bike's Clutch Slave Cylinder has simply lost its ability to slide smoothly along the inside the machined aluminum housing of the Clutch Slave Cylinder barrel. Remove Clutch Slave Cylinder assembly, disassemble, clean all parts, the replace rubber parts and the return spring, reassemble, refill hydraulic fluid, bleed system, ride. Here's what the Clutch Slave Cylinder looked like on my '99 5th Gen VFR: Question: How smoothly do you think the Clutch Slave Cylinder's internal piston was sliding with this 20-year-old brown muddy goo in it? (Not to mention the fact that the rubber sliding-seal on the Clutch Slave Cylinder's piston was also 20-years-old and pretty much hardened up instead of soft and supple as a rubber seal is meant to be) And... this is what I found inside my bike's Clutch Master Cylinder: Cleaned and refurbished:

Under the heading of "This works for me, your mileage may vary..." I have an improvised technique that I've used for years on things like this (oil pans, clutch covers, stator covers, and anything else that's stuck tight to the bike due to old gaskets). I've got a couple of small "slide hammers" that I use to gently free items like these from the bike (I think one came from Harbor Freight and the other is from a bicycle shop years ago back in my mountain biking days). In every case the manufacturer has provided little tabs of metal around the perimeter of the oil pan or cover that I'm working on. Both of my slide hammers have a threaded insert at the end and I've installed a wide-crowned bolt into that end, onto this bolt I've pressed a soft aluminum crush washer to insure that I don't cause any damage to the cover tabs. I hook the the edge of the bolt+washer over one of the cover's tabs and give the slide hammer a couple of pulls then I move to the next tab, and so on, even if there's no perceivable movement, I just keep going gently around the tabs until something gives. Eventually this action frees the cover from the bike.

It appears that (according to page 4-6 of the 1998-2001 Honda VFR800fi Service Manual) the Honda-factory-applied "mastic" you're dealing with is Three Bond 1207B which is really just garden-variety RTV Silicone (RTV = room temperature vulcanized). I don't know if I need to mention this but heat is always your friend when you're trying to remove things with tightly seized surfaces. It might take a while to gently heat up that big piece of aluminum (the entire oil pan) but it might do the trick of making the substance in the joint-line a bit more workable.

If I'd done what the Original Poster described (in his original post) I wouldn't want to remove the sump if I could avoid it. I'd also be concerned about the condition of the drain bolt threading in the sump. Here's a possible course of action: - Find and purchase a properly sized thread replacement (Helicoil or Permacoil or Timesert or whatever type you decide is best for an oil sump) - All of these thread replacement methods have you drill out, to a slightly larger size, the original thread-hole so it can be re-tapped to accept the thread replacement insert - So after doing the drilling out part of the work to prepare the oil sump's original thread-hole for the insert, you pause to use a magnet to fish out the broken drain bolt piece - Then continue with the process of installing the thread replacement insert - There's information available on the web about how to control or catch the shavings or bits of oil sump that might be generated during the work

It's 2019, we've reached a point in history where our access to photographic technology is ubiquitous. So... "pictures or it didn't happen" certainly seems like a reasonable expectation when something as bizarre as "the bike has/had an oil leak but a wasp nest just happened to be in exactly the right spot to prevent that oil leak from being noticed" is proposed as an extenuating circumstance encountered during maintenance. (that said, I've actually seen wasps do some amazing nest-building: Around about the late 2000s the Oakland International Airport extended the length of one of its terminal buildings. The Airport Authority didn't realize it but this extension of the terminal put the far end of the building out into an area populated by a type of "mud-dauber" wasp. When the aircraft gates at this far end of the building opened up for use we experienced blocked Pitot Tubes (the orifices that allow the airplane to sense airspeed) because the wasps were building their mud-based nests inside them, sometimes the wasps would build these nests so quickly it would happen to an airplane that was only at the gate for about 40 minutes)

Check the wiring harness ground point (usually to engine somewhere), partial or complete loss of path-to-ground can cause weirdness.

Sounds like you've got 2 "wants" that are pretty much mutually exclusive. You want to own/ride a well-sorted motorcycle, but it also sounds like you might be on a tight budget. I'm also very OCD about only riding a very well-sorted motorcycle and I've refurbished 2 5th Gen VFRs. I can tell you that bringing a 5th Gen (a bike which is now 20 to 23 years old) up to a good standard costs a pretty good amount of money, which leads me to say that maybe a newer year model bike would give you a situation that wouldn't require as much maintenance and thus cost less in the aggregate (cost + maintenance costs). (Here's the forum thread that I created while refurbishing my first VFR800: https://vfrworld.com/threads/refurbishing-my-99-5th-gen.52488/)

I'll never understand the unwillingness to do a valve check/adjustment on a 5th Gen. I enjoy doing this bit of maintenance. With its gear-driven cams and the shim-under-bucket clearance method the 5th Gen presents a very straight forward and hard to mess up situation (unless basic math is truly not your friend). And there's no cam chains to fight with, and no cam chain tensioners to worry about. Just mark the gears so they can be reset and re-torque the camshaft hold down bolts in the correct order when you're done. And getting down through the bits that block your access to the cam covers is a great opportunity do a few other things: to check/replace the spark plugs, to replace a 20-year-old thermostat unit (and all of the O-rings and associated hoses), maybe go ahead and pull the injectors to send them out for testing/cleaning (as a 2nd or 3rd owner you just don't know what quality of gasoline the bike has seen over the years) and maybe replace that 20-year-old fuel filter while your at it.

What I meant to indicate was that the sound might be related to the intake flapper not operating properly.

If I remember correctly, on a bike that is otherwise fully functional, that sound might be related to the intake flapper.

You may notice that those of us who are previous customers of Daugherty Motorsports will mention "rebuilt" rear shocks from other Honda models (929 and 954). That was how Jamie Daugherty used to operate, rebuilding and modifying these shock to new (better) specifications to be installed on other motorcycles like our VFR800s. Now Jamie has moved on from the 929 and 954 shocks. He's offering his own new, custom built rear shock under the name "BD40" which he is producing to customized specifications for a number of different motorcycles, including our 5th Gen VFR800s.

Here's a short video somebody made explaining the wax unit on a 6th Gen VFR: https://www.youtube.com/watch?v=k4oVVbzTvVo

Terry, doesn't the wax core expand when heated, and contract when cold? Unless you're skipping part that in your explanation and jumping forward to the part where the contracted wax core pulls on the starter valve control mechanism which holds it open, and when the wax core warms and expands it relaxes its pulling on the mechanism.

I'm out traveling right now, won't be back in Denver until late Thursday night, hoping that Aurora Honda takes really good care of you and your VFR (they've alway been good to me). Let us know how the maintenance goes.

I didn't know you were without a Service Manual. There's an electronic copy of the Service Manual available here on the forum. The MAP sensor is attached to the bottom right-hand side of the airbox. The white sensor on the bottom of the airbox is the IAT (intake air temperature sensor).

Those two holes admit air into the Starter Valve system. Nothing cosmic going on there, just make sure you get them reattached as you're putting the airbox back on. After you get things reassembled you're gonna need to do a Starter Valve Synchronisation, see the Service Manual on page 5-67. That will help to sort out the stumble in your off-idle acceleration. When you're putting the airbox back onto the throttle body you want to be very careful to make sure the MAP sensor is connected properly.

wow, that '01 5th Gen is beautiful.

Before you blame the wax-core warm up unit as the (sole) cause for your bike's poor start-from-cold you should ask yourself: Have the non-VTEC valve clearances ever been checked/adjusted? Tight non-VTEC valve clearances can cause poor starting characteristics. What is the condition of the spark plugs? Are they original to the bike? Old spark plugs that are in the last half of their useful lifespan can cause poor starting characteristics. As part of my refurbishment efforts on my '01 VFR800 I replaced the fast-idle wax-core unit, just opened up the assembly that the unit goes inside of, removed the old unit, installed the new one and put things back together. No need to change any of the factory "white paint" marked items. Yeah, wax-core units don't live forever, they slowly lose their original range of motion, there's a lot of variation in longevity with something like a wax-core unit, some individual examples come off the production line at the high quality end of the spectrum and they last longer than others produced right along with the good ones, but there's a reasonable lifespan you can expect from this sort of thing and it seems like 20 years is "great" and slightly less is "good" and less than that is "fair". But whatever, the wax-core unit isn't hard to replace.

People who buy classic cars always say, "Buy the best example you can find." It sounds like you may have found a "best example." The 5th Gens are now at 20 years and older, even a super low-miles 5th Gen will require some work to bring it up to standards. Starting this effort with a low-miles "Garage Princess" instead of somebody's daily-driver is a great way to go.