after a bottom end rebuild i now have gear selection issues when my engine is running, yet i can select a gear when the engine is off with the clutch down and start the car and it'll drive ok but selecting gears is very difficult( ive got a 2wd cossie by the way)

now the only things i have changed while the bottom end was rebuilt was the fly wheel( i went from a lightened 2wd fly wheel to a refaced 4wd fly wheel and a brand new thrust bearing from msd) new clutch was re padded and my pressure plate was reconditioned

ive booked it into a garage to have it looked at as i dont have the space to take the box off but i have been asked if there is there any difference between the 2wd and 4wd fly wheels?