Just to be clear, do you mean that the knobs themselves look/feel wonky? Or is it that the stems of the encoders feel wobbly?
If it’s the knobs:
At the risk of stating the obvious, have you checked that the D-shaped slots on the knobs are aligned with the stems? It’s possible to put them on the wrong way. Even after removing and replacing the knobs countless times, they should still feel snug on the stem.
If it’s the encoders themselves:
Simply taking off the front panel and moving the UI board out of the way shouldn’t have affected them unless they really got knocked about during the repair.
Having said that, I do find the MD, MNM, and OT mk1 encoders noticeably looser than the later Elektrons. It’s annoying enough on my OT that I’ve even thought about de-soldering all them all and putting in nicer ones.