Terry

The first gear clunk is due to the clutch inner and outer spinning together when the bike is in neutral. When you engage first at a standstill, the clutch inner stops spinning as the gear is engaged (the clutch outer is permanently geared to the crankshaft so always spins), so that will produce some driveline shock. If the engine is cold the clutch plates are all stuck together with a cold film of oil and so the clunk is more pronounced when cold than when the oil is hot.

My first guess would be that you need a new battery, but you should check that the old one is getting charged while running by putting a voltmeter across the battery terminals. Unless you are seeing more than 13.5V with a few revs on board, the charging system could be failing. First place to check would be the stator-RR 3 pin connector, then I would also check the main 30A fuse, both are known to get some corrosion going which causes resistance and heat and can cause melting.

I resurrected a 1990 ST1100 that had been parked up for 10 years and thought I had a dirty carb fault as it would cough and fart any time I tried to rev over 4000rpm. Pulled those darned carbs out/apart 6 times! Turned out to be as simple(?) as a dirty electrical connector that was preventing the full 12V reaching the ICU, giving poor sparks at higher revs. Like you, I pulled every connector apart and cleaned it plus dielectric grease, along with the chassis grounds, and the bike runs like a new one now.

I replaced the clutch plates at approx 95000km because I was finding them to be grabby making a smooth take-off and gear change less perfessional-sounding than I liked. I'm very happy with the result, although I'm sure from a friction standpoint the clutch plates had plenty of life left in them. I fitted a shift star kit when I first got the VFR as coming from a Suzuki I found the gearbox pretty agricultural. I was really happy with the result and the VFR is a very sweet-shifting bike now.

There is also a bushing and roller bearing in the clutch that are easy enough to replace if needed. I did that on my VTR1000F as it had some movement (and noise). On my VTR I still have noise, and I think it is loose spring tension in the hub damper of the clutch outer. Apart form the noise the clutch works great.

The gear that drives the clutch from the crank is a split-style, spring loaded to take up the slack that can cause noise. If the clutch outer is incorrectly installed without loading up the spring tension in the drive gear, it will cause a bit of a rattle. But you won't know until you pull the clutch cover off and take a look in there. If you do take the clutch out out, you will need a clutch holder tool (although these can be pretty cheap).

Should only be held in place by friction of the plastic on the steel shaft.

^This is good advice. When you refill the forks, pump the cartridges to expel air, you'll be able to feel when you get smooth resistance. I would also just break loose the fork caps before removing them from the clamps, and do a final tighten once you refit them. This is a messy business, have plenty of rags and put newspaper on the floor; its very hard to avoid getting oil spread around.

Another vote for EBC HH pads; I have them in all my bikes. I also have aftermarket adjustable levers on all my bikes, the cheap ones from China, and they work great. Just make sure you order for the correct model of VFR (you don't want levers for a 98-01 VFR, but 02-13 should all be the same). In place of the factory tool for adjusting the chain tension, a big flat blade screw driver can be used to gently tap the eccentric adjuster around. Don't lose the steel loop/washer that holds the brake line in place at the pinch bolt, because without that the bolt can bottom out in the arm without putting the proper compression on the eccentric.

Centrestand technique is usually about pressing down hard on the foot lever, and lifting gently up and back. What will make a major difference to your particular bike is if the suspension has been lowered at all, because then you have an even bigger task. If you still have difficulty, you could try rolling the back wheel up on a small piece of plywood first (e.g. 1/2" thick) which will reduce some of the lifting required. I'm all for PAIR removal, it gets rid of a lot of messy hoses on a bike that already has too many, and on the 6G model with O2 sensors it may reduce any confusion for the FI system. I'm not a fan of flapper or snorkel mods, I think my bike pulls better at lower revs with the flapper in place. FJ12 is dead-on about the chain slack, too little will mean the chain is over-tight when the sprockets and pivot all align as the suspension compresses, and I suspect this damages the pins and causes tight spots. Personally I err on the slack side.

I think you answered your own question, if the brake works and the wheel isn't binding, and the pads are secure in the caliper, then you're good to go.

Just FYI, the 5th gen VFR uses the same front lever as the CBR1100XX 97-03.

The fuel pump on my 1990 ST1100 runs for 5 seconds when the ignition is switched on, then continuously when the engine is turning.

My view is the best place is direct to the battery terminals, but through a switching relay so that the positive connection is only connected when the ignition is switched on. I took a feed from a tail light wire to trigger the relay on my bike.

I replaced the friction discs in my 5G at 95000km. The clutch was working well enough (easy to change gear, no slip) but the take-up was getting grabby which was making take-offs less perfessional that I liked. With some new friction discs it feels like new again, a very smooth and easy take-up over a wider range. For the small cost of the parts and some of my own labour I thought this was well worth doing.