GreginDenver

Well now, that's an interesting opinion you have there. Funny that the Original Poster on this thread replied, "Outstanding. I will check it first! Thanks, Bill" to my suggestion that it just might possibly be something as simple and easy to correct as a mis-assembled brake lever. And this reply was made on September 13, 2018 which is now 6 months ago and he never returned to say that he hadn't been able to solve the problem. Whether the cause of the problem was actually a mis-assembled brake lever or something else, doesn't really matter, it seems that the Original Poster was able to sort the bike.

Sometimes what looks like a capped-off plug is actually a diode. Or possibly a plug-in point for diagnostics.

This might just be my (somewhat OCD) perspective, but if you're gonna go and refurbish the front forks (clean-out, seals, sliders, oil), maybe you should look into the Daugherty Motorsports Fork Cartridge Upgrade Kit? http://www.daughertymotorsports.com/product/fork-cartridge-upgrade-kit-1998-2001-honda-vfr800/ I've done this upgrade on both of my 5th Gens, ooooooh so plush and responsive, makes the bike feel lighter somehow.

And here's a +1 on choosing to use the heavier gauge wire (if you're gonna do a wire-it-yourself job with an improved R/R). Honda's wire size choices on the VFR (both positive and negative) weren't the best, which made the connectors prone to overheating and melting (if even the slightest amount of corrosion developed on them), and this sometimes produced a knock-on cascade of even worse problems like stator failure. There's even a product called "The VFRness" that a lot of guys (including me) have used to improve the flow of electrons through our VFRs.

Amazing bike. A year and a half ago I purchased an '01 with just under 12,000 miles on it and in situation similar to yours because it was also in amazingly well-preserved condition (for a 17+ year old bike). This like-new '01 was my second low-mileage 5th Gen VFR purchase (the other was a '99 with less than 19,000 miles). I mention this because with both of these bikes I found that great condition did not also mean great maintenance and upkeep. Both of my 5th Gens had the original fork oil in the forks, probably the original brake fluid (maybe "topped off" at some point, but obviously never flushed and replaced), same story for the hydraulic clutch's master and slave cylinders, also both bikes still had their original coolant thermostats. And the list of "deferred items" went on from there. Just saying congrats on the beautiful bike, but beware, those good looks can hide a lot of things that really need to be addressed.

Repacking is an art (or black magic). I've done a few over the years. Within the range of what the manufacturer qualifies as a "properly repacked" exhaust canister there is room for some tuning of the sound output, a little tweak of the canister's basic sound characteristic. A little more/tighter packing = more harshness/bark. A little less/looser packing = more lower register/less harshness. I've got my '99 5th Gen's Vance&Hines S4 canister packed on the tight side for more bark.

Once again, the 5th Gen VFR air box has 2 intake paths for a very good reason: from idle to about 7,000 RPM the rubber snorkel provides a level of airflow which causes the air box achieve a resonate frequency in that RPM range. When the air box hits a resonate frequency it boosts intake efficiency, which boosts torque in that rev range. After about 7,000 RPM the 5th Gen air box opens up the flapper. This changes the resonate frequency equation, moving the air box resonance point to the upper end of the engine's rev-range. Also, the 5th Gen VFR's rubber snorkel intake is long, which is exactly what you want for the lower end of an engine's RPM range. The Flapper side of the air box intake is short, which is exactly what you want for the upper end of an engine's RPM range. As others have pointed out, the 5th Gen air box acted in a similar way to the VTEC system in the later generations of the VFR (this also explains why the dual-path air box was dropped in the VTEC versions).

Great job, feels so good when your efforts actually fix the problem (and bring the bike back to running like it did when new). Job well done! The 5th and 6th Gen VFRs are getting older and, as you pointed out, things like the Thermostat and the Fuel Pressure Regulator are consumable items. The Honda build quality we love in our VFRs doesn't mean that the consumable items will last forever. I applaud you for addressing these things instead of trying to ignore them. I'm currently waiting on delivery of 2 Fuel Pressure Regulators, one for my '99 5th Gen and one for my '01 5th Gen. The '99 has begun to run a bit on the stinky side with not-so-good fuel mileage so it's getting a new FPR this spring. The '01 is fine (it doesn't stink of unburned fuel and the fuel mileage is still good) but I figure that while I'm doing the FPR replacement on the '99 why not do the '01 also?

I also felt that black was appropriate for my 1999.

The fuel pump unit that Honda used in the fuel injected generations of the VFR is a pretty robust and long lasting item. Before deciding that there's something physically wrong with your fuel pump I would first do an inspection and testing to see if the electrical connections at the bottom of the fuel tank are in good condition and then use a voltmeter to see if these wires are getting 12 volt power when you key-switch the bike to "On". Also, you should trace the wiring to and from the fuel pump connections to determine whether the fuel pump has a good path-to-ground (negative) connection to insure that the 12 volt power can flow in a normal manner through the fuel pump.

I'm a 5th Gen VFR guy so what I'm going to say may not apply to your '07 VFR (but I believe it does). Whether my little bit of information applies to your bike is dependent on whether Honda continued to use the same tuning principles for the PGM-FI system across multiple generations of the model (the 5th Gen VFR was the first fuel injected VFR so it can be considered to have set the VFR model template for the use of Honda PGM-FI). On the 5th Gen VFR Honda set up the PGM-FI system to use two completely different methods to determine fueling depending on the "demand" that the rider puts on the engine. "Demand" is most easily related to throttle position and the recent rate of throttle position change. While this description isn't the whole story behind "demand" it's good enough for a basic understanding. RPMs also factor into the equation. At low levels of "demand" the PGM-FI system uses the Manifold Absolute Pressure Sensor as the main parameter in determining the proper fueling of the VFR engine. At high levels of "demand" the PGM-FI system uses the Throttle Position Sensor as the main parameter in determining fueling. So, it something is whacked about your VFR's low "demand" (low RPM) operation the problem is very likely to be related to the Manifold Absolute Pressure Sensor. I get a lot of blow-back every time I say it, but removing the flapper and snorkel might have the effect of changing the amount of intake system vacuum the engine experiences during low demand/RPM operation.

27mm sounds like an accurate measurement of the sensor's tip-to-seat distance (1.063 inches), The pictures I posted (above, in this thread) are of a Bosch 4.9 (5-wire, heated) O2 sensor being installed into an Innovate Motorsports Extended O2 Sensor Bung which has a 1 inch total length, and in one of those pictures you can see how far the tip of the O2 sensor protrudes beyond the bung. In the top picture the extended bung has already been heavily contoured to fit tightly against the exhaust's mid-pipe section, but the upper-right hand end of the bung is still very close to the original total length. Sorry that the best picture I have (the top pic of the 3 that I posted) is a slightly angled viewpoint of the assembly and that this picture was taken when I was already well into the process of contouring the end of the bung so that it would closely mate to the outside of the exhaust's mid-pipe, but at least you can see well enough to get a good comparison of the lengths of the bung and the sensor tip.

I've been working on do-it-yourself motorcycle fuel injection projects for about 10 years now and the above post pretty much describes how I mount my Wideband O2 sensors. I always use an "extended length" O2 sensor bung. You can see in these build-up pictures how far the O2 sensor protrudes beyond the end of the bung (when you visualize how far it will protrude into the exhaust remember to include the wall-thickness of the exhaust header itself) . This amount of protrusion (or even a little less) allows the sensor to work properly.

If you're going to install LED bulbs in the turn signals you need to replace the flasher relay with one of these: https://www.superbrightleds.com/moreinfo/motorcycle-accessories/electronic-led-flasher-relays-for-motorcycle/787/842/