Tony
I went with a VM38 Mikuni from TD Hatrick, They supplied it all jetted to suit the following:
Cylinder was bored 87mm to suit an XR400 piston (96 onwards). This makes it to 420cc which I think is very useable and not over the top. This leaves very little liner, but once you are up for a re bore then you can fit a new liner with a bit more meat. You could then run oversize pistons as required.
The cam was standard XL350, ground to a sports XR75 Webb profile. What that means I have no idea, but seems to work ok.
Cam timing is retarded a couple of degrees. I think I worked it out to be about 3 deg but not sure right at the moment. As the cam chain drive sprocket is not keyed to the crank, inadvertently it was replaced slightly off line, and has proved to run to good revs like that. I have a vernier cam sprocket to dispose off if you are interested. We do not run any fly wheel other than the little rotor from the ignition kit.
I have had the head modified to run roller bearings on the cam. Again a successful mod.
I am not sure of the pipe diameter but think that it is up where you are heading.
As far as gearbox's go, I have done in third gear once. I think the biggest killer is coming down under hard power off of jumps. If you can control the urge to land under power I am sure the life of the gearbox will be extended. I had been looking at gearbox ratios for a while before I did in the 350 gears. I had an SL250 box which I removed the gears from and fitted to the 350 shafts. The 250 ratios are much closer together. I found that it was a better bike to ride and am hoping that the load on 3 and 4 wont be as bad.
I still run a cush drive back wheel. With the crap suspension we have and the lack of ability I dont believe the advantages of a light back wheel counter a longer living gearbox.
You could ask pretty well anyone in the WA club about the black XL and I think you will hear that it is pretty competitive. I have been impressed with mine and think with a good frame and better suspension they would be unbeatable (nearly) Other than that they are a bloody reliable, Long living, competitive and fun to ride bike. What more can I say.
Cheers
Steven