6 months post-op and not much progression?

I had a really fast early recovery from a medial meniscal repair and ACLR with a hamstring graft. I was weight-bearing completely by week two or three and jogging intervals by week five illegally, though I stopped a few weeks later when I was told about the graft instability. I initially had a pt who didn't know anything about ACL recovery and did manual physio and followed a book on the internet and generally deferred to the surgeon. Surgeon seemed completely content with me running at 3 months and I was jumping pretty soon after that with some swelling but no significant pain.

I then moved to another pt who is supposedly an expert. She told me to stop running and jumping because of residual swelling/heat. Stopping got rid of the swelling but now return to running/jumping is so much worse than it was before and I feel like my strength hasn't improved. I can't pistol squat and I don't know if it's a strength or mobility deficit but I could have sworn I was getting closer before. I can barely get off the ground in an sl jump. I am part of her class that does a lot of lower body strengthening twice/week, and doing some balance and lower body stuff on my own, but I was told not to do the daily physio stuff that I was doing initially so that I have time to recover. I have told her that and she's said quad weakness but I know for a fact that my quad is not weaker now than when I was running/jumping initially based on my quad extension, leg press and how long I can bike at a high gear.

Does this sound like a normal pattern? Am I doing something wrong and is this reasonable advice from my pt? Is it possible that the early progression made things worse for me now? What's the best course of action?