Please read down the page about seven threads to "Header Installation", most of your questions on header install are answered in that thread. You are not replacing gaskets between header and engine because, as explained in that thread, it is a stack of thin stainless plates, not a crush gasket that gets worn out. And gasket from exit of stock header is transferred over, see instructions and pics in that thread.
However, if jacking the motor on the header side to replace the motor mounts anyway, that will indeed open more space for header swap than we normally get with just tilting alternator forward. So, indeed those two projects are good to combine.