hi aquinas! i'm a bit late to the thread, but i wanted to chime in because it all sounds sooooo familiar!
when DD5 was your son's age, she also had many of these issues. it really puzzled me at the time, because it seemed like she was a complete magnet for too-much/too-close/too-aggressive attention. she did all the stuff your DS has done to try to explain to the other kids that she needed time and space, but no matter how clear she was, she still routinely needed adult intervention. as it turned out, the kids (even the 6 year olds at her Montessori) were simply too small to really hear her.
Pre-K was, unfortunately, more of the same. every single kid seemed to think that DD was her One True Friend, and yet at the same time DD reported feeling completely isolated, frustrated and angry. the good news is that her dance buddies (8ish) are a whole other story. they get her - and she gets them, so like HappilyMom said, the early years really were very difficult.
during that awful time, we did manage to befriend a family with kids in a range of ages - we didn't do it on purpose, but if i could have planned it, i would have! the beauty of a whole mess of kids is that everyone could take turns playing together and it frankly seemed a bit more natural than trying to forge a friendship between my 2 y/o and a 6 y/o from school!
oh! and i just remembered an observation DD once made about "park friends" that might help. she said that park friends are not the same as real friends. they can be ok to play with, but you don't know each other well enough to know what might upset the other person. over time, i've seen her use this insight to get over conflicts that she didn't see coming - and i think it has helped her a lot. of course, she's totally given up on age-peers at this point, so her new park strategy simply involves finding a younger kid to "play" with as a gateway to chatting up the parent(s). your DS is a bit young to employ that one yet, but... maybe next year? he'll totally be the big kid to all the 2 year olds playing in the sandbox with their parents!
and btw - i completely empathize with you on that "cute" comment - DD used to announce she needed to "go away to manage her feelings" in that kind of situation and i've seen a few of those responses, too. they made me want to SCREAM!
