What is his CBC(white cell) count? If it is low (below 5) it could be an immunity issue. We have a Trakehner who battled with similar symptoms...he's on an immune booster and doing much better now.
Also, don't forget to check for thyroid disease. The thyroid controls so much of a horse's (and person's!) body. There are lots of treatments available if it is hypo or hyper thyroidism.
I noticed also that you said he is being fed cracked corn and alfalfa. While high in starch (the corn) and protein (the alfalfa), there are little vitamins and minerals available in those feeds. I would probably look into a vitamin/mineral supplement focused on growing horses - or purchase a commercial feed that has them on the ingredients list. You've gotta take your vitamins to grow big and strong
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