I had a similar problem when I ran 5/3/1 as well. I couldn't get past the 300 squat mark and everything didn't fall into place.
I swtiched it up and started the cube method for a little over two months. I found the variety of repetition focused days with heavy and explosive days helped me with a lot of things (Squatting below depth, better form, more power, especially in the hole).
My advice is to run things until they stop working for you and try and find a routine that works well. Run the cube, see how your lifts go (Keep in mind you only go for a 1RM when you know you can hit it perfectly) and see where it goes. If you're still stuck, there are still a tun of routines out there. (http://www.joeskopec.com/
) That site has calculators for almost every routine out there right now, including a lot of the russion high volume ones.