I had my block built for boost but cracked a sleeve. So i picked up another block to build. The main caps look really rusty that came with the new block i got. I was wondering if it is ok to take my main caps off my old motor or does this usually cause problems by miss matching?

 

would need to be line bored

 

Yep, too much of a mismatch, so you would need to bore and hone the mains. You would actually be better off just cleaning the rusty caps (unless the mains are jacked up anyways). Usually some WD40 and scothbrite is all it takes.