"The first three wound boxes have temporary penalties that apply only to your next roll"

1) Any roll at all?  Positioning, etc.?

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"Temporary penalties stack up...Lasting Penaties don't stack together"

That's fine if I only have temporary penalties or if I only have lasting penalties, but what if I have one of each?

2) So if my #4 wound box is checked off (lasting wound, -1 to all rolls), and then I get three wounds so the #3 wound box is checked off (-2 to next roll) will my next roll have a penalty of -2 or -3?

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3) I assume that advantages, enhancements, etc., cannot raise a die above d12?

1) Yep. Any roll at all. I've heard some people house rule it to "your next attack or defense roll" and that's fine, too.

2) -3. Temporary penalties stack with lasting.

3) Yep. d12 is a big as it gets.