CBR 600F gearbox

The other day I started changing the transmission kit on my Honda CBR 600F because it was due and it was also making a strange noise. To my surprise, I discovered the noise was coming from inside the gearbox. When I put it in first gear (without transmission), the output shaft jerks, whether in first or any other gear. Does anyone know what could be wrong? I think I'm going to have to remove the engine and gearbox. Any advice?

Thanks.