When you reinstall the cover, and the bolts aren't tight yet, tap it upwards and hold it there until you've tightened a couple of bolts; just a few thousands seem to make 1st/2nd difficult to engage after being in Reverse.
Obviously you don't want the shift levers to rotate out of alignment, check in neutral using a 1/4" shaft or drill bit in the shift tower where it's notched and make sure it slides through the provision in all 3 levers.