TDI 200 Manual gear box problem

I drove my tdi 200 apparently without gear oil.. gearbox got stuck in gear no 3.. Drop the gearbox and found 2 bearings in the gearbox need to be changed.. fit back the gearbox.. shifting the gear with clutch depress everything normal.. once the clutch released, gearbox is noisy.. I had a new clutch bearing fitted.. so cant be the clutch bearing.. when i start to drive there is sort of knocking noise..
Could it now be the transfer box? What do you think is wrong with the gearbox system?
Rgds.
Ham from Brunei