Thanks a million for all the tips guys, will let you know what happens. All the head bolts were within 2mm so I'll go with them and CAREFULLY clean out the threads with a tap. Mark, at the machine shop, said the guides for the intakes were o.k., however the exhaust guides were out of tolerance. Regarding the injectors, the car was running great other than overheating on mountain roads, so I'm guessing the injectors will be fine maybe just cleaned up a bit.
Matt