Yikes! Sorry to hear your son is so sick. I can't really speak for all the symptoms, but we just go over HFM a couple weeks ago, and my son did have the rash over his entire body. The ped said that the only "consistent" rash of the HFM is the hands, feet, and mouth (I know, duh!), but that the rest of it really differs from kid to kid. My son is fair with somewhat sensitive skin, so he gets rashed pretty easily. With HFM, it was all over. He also had a MAJOR loss of appetite, and was really cranky. Most of that was due to the sores in his mouth, and because of all that, he also had trouble sleeping. His fevers weren't that high (only around 100), but hung around for a few days. We also thought he might have had an ear infection because many of the symptoms seemed the same, but he didn't--the poking at the cheeks and ears were because of the pain in his mouth (and a little teething).
Was your son on augmentin? Whenever mine took that it helped the infections but they would get diarrhea, too. Once we upped the yogurt intake from 1x/day to 2-3x/day, they were both fine. Now when they take that we just give them more yogurt (YoBaby and YoKids) right away and they never have any stomach issues.
As for the other stuff, I'm sorry I can't be much help. I haven't heard of the eyes and diaper rash being part of it, but that doesn't mean it's not. :) I will say that if he did have diarrhea, the diaper rash could be part of that, but I don't know about the eyes. My kids tend to get the "perfect storm" of stuff, too, so I tend to worry they've got more than one thing at a time. But as for the HFM, much of your experience sounds consistent with mine. Good luck!!!