He could have injured his shoulder after a jump.
Before stopping your horse for months at a time, or spending a bunch of money on expensive tests, call a chiropractor. If he can't help, then stop your horse.
Well recently we decided that since he was going to be in the stall for so long that we could at least take him out for a walk and grass everyday while drugged. So at least he's getting out. I'm currently at school so i'm not able to see him but every 2 weeks, when I drive back home.
I second the chiro idea. A good chiro can give great insight. From your description it sounds like it's preimarily a check ligament issue. Have you tought about trying magnets? They can work wonders. Also considder swimming him. It's a great way to get them safe exercise and can help keep them sane while not in work. We have a few horses that we race out of the pool. No track time at all...just swim, race, repeat!
Well the chiropractor came out and spent hours working on him. A bunch of things were out of alignment but his scapula was the worst apparently. It didn't fix his lameness, but the chiropractor agrees with me- My horse's muscles are extremely atrophied. The chiropractor also thinks that my horse also may have a nerve entrapment in the leg.