I'm about to pull the heads off of my core motor in a few minutes. Can I magnaflux aluminum heads? I want to check for cracks. Also, what other measurements should I be aware of? Spring rates seated and "over the nose", cam lobe heights, etc.

No, you can't magnaflux aluminum heads. Here is a link that describes how to check aluminum heads for cracks:

http://classic.artsautomotive.com/crackcheck.htm

You should also use a straight edge across the head to check for warpage. I don't know what the tolerance is for subie heads though.