Well, I picked up the VFR gearbox this afternoon and disassembled both the VFR and CBR gears and lined everything up.
As Dan mentioned in the other thread the VFR and CBR input shafts aren't interchangeable. Bugger. Here is proof.

VFR shaft on top, CBR on bottom
So i've gone with the standard CBR 1st gear (no choice) and put in the VFR 2nd and 3rd. Lets face it, you don't use first gear when racing very often.
Here are the two gearboxes dismantled and side by side. Cbr on the left, VFR on the right. Notice the VFR doesn't have a 5th gear pinion on the output shaft. Hence why it was sold to me!

Here is a list of the pinions I used from which bike written in the order left to right as seen in the crank case;
INPUT SHAFT
2nd VFR, 6th CBR, 3/4th (integral) VFR, 5th CBR, 1st (integral with shaft) CBR
OUTPUT SHAFT
2nd VFR, 6th VFR, 3rd VFR, 4th VFR, 5th CBR, 1st CBR.
The reason there is more of a mix and match than you might expect is because the shape of the gears dogs that interlock on the output shaft are slightly different from VFR to CBR, and I have tried to keep the interlocking gears from the same machine to avoid any damage.

Could you get a machine shop to mill down the VFR shaft ?

I'll be asking about that when I give my crank to the engineer. But the hardening on the first gear and splines might not take well to it. I'll let you know.

Send it off for heat treating or cryo afterward.

Greggo, glad you could get some use out of it!

Not much to update you on. Except forget the crappola above about the gearbox, the VFR output shaft will be getting machined and cryo'd so I can use the VFR 1st gear.

So the Crank and Gearbox are off having 'the frenchman' work his magic apparently, and I will be ordering my pistons and rings soon too.

Big Bucks ???

Maybe GFORCE should try cryo on his cranks that keep snaping?

Getting it done at a most favourable rate.

Greego, just small question. Are you going to use NC23 engine exhaust cam ?

Parus, I don't know to be honest. It will depend on what I learn on the dyno with the current engine - once I get the time, parts and money together to get back to the tuner.