Jeff,
The studs and bolts holding the two manifolds together are notoriously rusty/busty dudes. Lots of heat and penetrant along with some careful wiggling and loosening will usually get them loose. There is a gasket between the two manifolds that should be replaced when you are putting all this effort into this project.
My advice would be to do whatever it takes to get the two apart, clean up that sealing surface well and install a new gasket. Clean the mating surfaces with a file and make sure the bolts are not rotted off from exhaust gases. Reassemble both manifolds when they are clamped to the head and tighten the bolts that mate the two.
After all this is aligned and tight, take them to the automotive machine shop and have them milled as a pair...don't move them again, and make sure the machinist has done this before and knows what the desired outcome is suppose to be.
This is a real simple job if it is done properly...it is frustrating and a waste of time and moola if it is done wrong...do it right!
Don't forget that the alignment rings might have to ground down to allow the manifolds to mate properly if gobs of material is taken off at the machine shop. Lots of folks recommend replacing the two outboard alignment pins with threaded studs to help pull the ends of the assembly snug to the head. Sorry for the extended novel!
Stuart
