Jen,
My son has Aspeger's and I can tell you that any major change in schedule creates a lot of tantruming and crying and random meltdowns that seem to come from nowhere. You just started Homeschooling, that is a huge schedule and life change. It is possible that your son's meltdowns have to do with dealing with this new schedule. Like everyone else says, I would hold on and try to take it easy. Let him relax a bit and don't be so hard on yourself when he tantrums.