If your particular assistance work has helped, then that’s fine. I would still recommend you only hit the prescribed reps on some days, especially for the DL. I had issues with full recovery on 5/3/1 when I was trying to do it 4 days per week. I had a similar experience myself with the DL on the program and I asked Wendler himself about it over at the elitefts Q&A.
He basically said I needed to choose my battles more carefully and only go above the prescribed reps on 1-2 exercises per week. He also said he has found the more advanced a trainee is, the less often they should go for rep maxes. I would try a cycle or two where you only go above the prescribed reps on the DL one time per cycle and see if that helps refresh things a bit.
I’m also assuming nothing else has changed that would affect recovery (diet changes, less sleep, more life stress, weight loss, etc…).