I'm playing a Cleric, and I wear heavy armor. Suppose I reach the armor cap-- do alteration buff spells take you past the cap??

not afaik

I would think not..but you never know it is skyrim.

The armor cap is 667 armor rating, you get a +25 hidden bonus from every armor piece you are wearing, so with 4 armor pieces the cap is 567.

Any armor rating above 567 (with 4 armor pieces) is pointless, all the alteration flesh spells do is add armor rating.