i dont know a great deal about 330CI, but typical things you check before going into the gearbox include:
-gear linkage bushings and assembly (sounds like you have done that)
-clutch master and slave cylinders, rebleed the system
-clutch adjustment for pedal play/throw, make sure that its actually full disengaging and fully engaging the clutch.
-make sure the car actually has the correct shifter arm? sounds like it could also be some homebrand short shifter from a different car?
the type of issue (cannot select the correct gears?) does not sound like an internal gearbox problem at all. Many shops when they see a euro car just see $$$ and wanna do as much work as possible to milk u dry