The cleat and saddle position is the most valuable thing you can glean from a bike fitting, be it retul, specialized bg, or something else...

You can move your bars back towards their original position over time. I've had a few fits in my day (discounts in college for collegiate racers), and they all put me in a wayyy upright position. I increased the length of my stem and drop very slowly over about 6 months, with atleast 1 month increments between any change.

Also im not sure how aware you are of the diagnosis of your injury (overuse injuries are tough to diagnose), but FWIW I have quadriceps tendinitis, and have for about 4 years. I came home from college one winter and tried to do a 18/20/22 hour/week three week block while lifting and working on my feet during the day and not recovering, plus no stretching.

Your problems will likely never completely go away, but like mine, they will be under control if you rest as much as you can stand now and be diligent about stretching and PT. Don't jump into riding and training too quickly and cause yourself a more serious chronic issue.