Assuming evrything worked fine before you took the cover off, it sounds like something is jamming inside the shift box.
1. Take the shift linkage loose from the box, using each shift linkage only, check that the trans will now shift. If it does, place trans in neutral and go to step 2. Leave shift linakge disconnected. If it doesn't, fix jam inside trans.
2. Disconnect the shifter rod from shift box at coupling above shift box, check that shifter moves thru all gear positions. If it does put shifter in neutral and go to step 3. If it doesn't fix or replace shifter.
3. If shifter moves correctly, remove shift box cover and unjam internals. Put shift box in neutral, reconnect shifter rod and shift linkage. Check that you can now shift thru each gear.
if you're not sure how the internals of the shift box should look correctly positioned, let me know. I have a spare box I'll take the cover off and take a photo and email it to you.
