As CMSMJ1 says, bleed the brakes and the front master cylinder. I have also been advised that when you change pads to a different make you need to wet and dry the discs with a very fine grade paper to remove the surface film.
On the gear shift thing i would try changing the oil first and checking the old oil very very carefully for any metalic flakes or debris. i had similar issue with my 30 box, it would jump from 2nd into neutral when trying to get 3rd. i think it was the little dowel pin (part 34) that had become worn.
http://www.cmsnl.com/honda-rvf400rt-nc3 ... ml#results
I prefer the 35 box myself as the first gear is shorter and it's faster off the line, but if your not doing racing starts i would stick with the 30 box.
I use the gixer rotor conversion rather than running total loss it's much better than standard and you keep the battery charged.
) as predicted i am hooked 
but it appears i have a few problems with the bike first brakes are good but i feel they could be better whats the best route to go is a fully serviced standard setup up to the job with the right pads(which)or should i look to changing calipers/discs if so what 2nd i have a problem with 3rd gear on warm up lap not riding changing gear hard bike lurches in 3rd its not pulling smooth when changing hard its stays in gear for a split second then hits a neutral and i have to go to fourth (not good 
)any ideas or shuold i just find a 2nd hand box is a nc35 better anyone got either for sale cheap if new box i understand it can be done without taking topend off is this ok or should i tear it all down also running total loss how long should a battery last any other improvments i could make bike is trackday use only
