Working Out with a Shoulder Injury - If it hurts, don't do it

So, I over worked out my shoulders and rotator cuff, an I ended up injuring myself. The first thing I had to do was completely stop working out for 2 weeks, limiting myself to walking outside, because there was no exercise in any format (abs, cardio or strength) that didn't hurt. Even sleeping and sitting on the couch hurt my left shoulder.

Subsequent to the hiatus, I have restarted my workouts. The first thing I reintroduced was low-impact cardio with significant modifications on my left side to not irritate the injury. Second, I reintroduced moderate and strenuous cardio, but I still severely limited movement of the left arm (I know it created some imbalance, but I wouldn't have been able to do anything otherwise). I was able to make burpees not hurt by doing the "down" part low impact, but putting a jump on the "up" part.

Third, when it no longer hurt to hold weight on my left side, I reintroduced Lower Body Strength workouts. The one thing I make sure to avoid is resting weights up on my shoulders. Finally, I have recently reintroduced upper body strength exercises. I use very low or no weight on shoulder exercises like lateral and ventral raises, as well as pec flys, which I cannot do properly with weight at this time. The biggest bummer is that I have had to give up pushups for a while. I spent a year 7 years ago getting myself to the point where I could do 3 sets of 30 plank pushups. Today, for the first time in 2.5 months, I attempted pushups from my knees. I surprised myself by eking out 10 pushups. I wisely decided to skip the second set when my shoulder really started hurting.

The one thing I will probably not reintroduce is cardio kickboxing, although it is my favorite cardio workout. I think this type of exercise, in combination with too heavy weight for certain shoulder movements, is the cause of my injury.

If anyone has worked through this type of rotator cuff/shoulder injury, I would love to hear how you regained full use of the joint, including strength and range of motion. I am really trying to avoid surgery.