I had taken my gearbox out because the speedo drive fell inside

the specialist got the speedo drive out and rebuilt the box. 020 gearbox 5 speed
I have just put it back in the car and when I put the clutch in it there is a loud sound like something is catching in the box. (sounds ok when clutch out)
its had new bearings including release bearing, oil change, ect, any ideas anyone??
Also there is a rod that goes through the gearbox (at end casing) with a spring on the end that has come out and wont go back in!!! ahhhhh
