So I thought I would update again - since we went back to have everything checked out as the vet requested after one month.
What I did during the month: I followed the vet's directions to the "t", minus having him in an indoor stall. The outdoor stall was not much bigger than an indoor stall and it kept him happy - so that worked out well. I wrapped his legs for two weeks. I also iced his legs twice a day (once before work and once after work) for two weeks. I also put him on Recovery EQ and eased him into it as directed on the package.
What the vet did/said/found: I am happy to say that the vet was thrilled at my horse's recovery. When I brought him in originally he was level 3 lame, and this time he was completely sound. We did the lameness test (flexion test) and put him in the round pen as well. I pushed for an ultrasound even though it wasn't necessarily needed. Everything in the ultrasound came up completely clear and healthy :)
Next steps: I chose a very conservative recovery process (which may not be necessary, but he is young and I have time - so why rush it right?)
*For the next 3 weeks we will do walk/trot for 30 minutes (5 minutes walking, 5 minutes trotting, etc.).
*If all goes well we will add the canter into the work out and increase the time to no more than 40 minutes with the same pattern - walk 5 min, trot 5 min, walk 5 min, canter 5 min).
*In 3 months if everything is going well we will slowly start adding jumping back into our routine.
That's it for now. Hopefully this helps people out with similar problems - though I still stress the importance of going to the vet. Well I cannot say for sure that it helped, I am a big fan of the Recovery EQ, and now that my horse is on it, I will continue to use it.