Ouch. I can relate to all this.
I tore the rectus femoris muscle while practicing martial arts, along with two abdominal muscles on the same side. Was fine through the workout, but once I quit the workout, I could barely walk out of the dojo. It's been haunting me ever since - some days I don't feel it, others it tears me up.
I've been doing alot of research for injuries like these. One thing that helped enormously was active release. I've had it done on my rotator cuff a long time ago - well worth looking into. As well, I'm curious about prolotherapy - there seem to be a few people that swear by it.