I see that front of your rocker is properly aligned to the cowl, and that the rocker is parallel to the top of your wheel arch.
As such, the only solution I can think of is for you to lower the quarter panel. The curved part in your second to last pic is going to hit the rear cross member, so you're going to have to carefully cut that area out (save the offcut), tack your quarter panel in such that it lines up to the rocker, remove material from either the offcut or the quarter panel, and weld the curved peiece back in.
Sadly, from what I understand, these replacement panels almost never fit right. You have to deal with modifications like this as part of the normal course.
I bought my quarter panels from Real Steel. I had a different problem- the ambulance door opening was out of square by over half an inch from top to bottom, so I had to do a pie cut and weld it back together to get it square.