have you pulled the box out again yet?
once you do, photo / video as much as you can, turn the input shaft by hand, do you feel resistance like metal grinding the input shaft will turn easy enough once its out. Have you taken your clutch apart? ( get a clutch alignment tool) photo/video the clutch components too as you may have a broken spring on the clutch disk, take the thrust bearing/shift fork apart, look for cracks on the shift fork, clean the shift fork first.
When driving the car you you have any problems in any of the gears? does it move in and out of ALL of the gears without a harshness?
I know you dont want to pull it out again, but dude i have just taken the box out of my car and put it back in twice, twice because i resembled it and forgot to put a bearing and spring in... would not stay in reverse.. sucks but if you want to have "boy racer" cars and thrash the crap out of them then this sort of thing is what you have to put up with, they break