Good question. I was wondering the same thing. I'm guessing that "machucar" means that something hurts something else (is an active verb), whereas "doer" is a passive verb (my head isn't hurting anything). As botas machucam = The boots hurt. The boots are hurting my feet. The boots themselves don't feel any pain.
Anyway, this is just a guess. I don't know for sure.
That's pretty much it; machucar implies action - usually physical, but not necessarily so; doer implies reaction - something hurts.
You just forgot to mention the reflexive use of "machucar" (Eu me machuquei - I hurt myself [past simple]); in this case you hurt yourself, but there's still an agent-patient relationship at work (Who/What did the subject hurt?) that's entirely missing from "doer".
I'm not really sure. For me it sounds really good (and that's actually the first possible translation that came to my mind when I saw the question), but I think it's a little more informal. But in my opinion, it still sounds right and I believe it's a good translation to "minha cabeça dói tanto" (especially, if you're emphasizing it, like, with exclamation points or something like that).
I think the best (but not only) translation for "TOO much" would be "demais." And that's because "demais" basically means something that's like waaaaayy more (satisfactory, unpleasant, painful, or anything else) than normal, you know? So after all, I think "demais" is more than "tanto," just like "too much" sound more than "so much."