NC29 unknown fault help needed,

[weedossmc]

Hey oop peeps. need help with weird fault, sixth gear appears to momentaraly jumps out off and then goes back in just as quick. (many moons ago second gear went on a cbr 400 i had, and there was no mistaking that it was fuc*ed). Recently i have just finished a partial engine rebuild cause i thought my gear box was on it,s way out so i fitted a gear box from a low mileage bike (mileage was verified and it looked great, no rounding of dogs or slots compared to mine).
other things such as valve oil seals, valves reseated, bearings, races and other thingys were changed, piston rings were still well within limits, an engine compression check before and after confirmed this.
sync tests were out before test but were spot on after rebuild cause there were ticking noises coming from either the R.H.S carb or valve shims (some were out but after rebuild some were replaced and again were spot on).
but after the first test ride (within 10 miles) the sixth gear prob came back along with the ticking noise (shims rechecked and were still perfect???).
The carbs were cleaned up cause they were dirty inside but after cleaning were fine all pilot holes breating holes etc were all cleaned and blown through with a air compressor, i could see and prove that all holes, passage ways were clear and after another sync test was perfect along with the air/ fuel mixture. i was,nt too sure off the jet needle, needle jet appeared o,k.
please help cause i,m bursting to get out on my bike after a short illness.

[leopard_pagan]

ticking is probably the fuel pump, it is quite loud.
6th gear could be caused by a worn out gear selector fork.

[weedossmc]

Hey L.P Never thought about the fuel pump, the ticking actually sounds as if it,s coming from the R.H.S carb valve which is above the fuel pump?. I,m using one of those stethascope thingys. clearances are still ok. The only thing i can think of just now is that it,s either the clutch somehow or a carb problem cause it seems to happen more when under accelaration/load.
i,m just gonna keep using it in any case.
cheers L.P