I know this is an old thread, but I had to do this to my '97, so will pass on the experience, being that eXoR never got a response.
When my driver's side exhaust manifold to down pipe stud broke, further inspection showed a crack at one of the flanges and the need to replace both cast iron manifolds. The truck had over 190K miles on it at the time and with the weather being what it is here in the Northeast, nuts, studs and manifolds were all welded to each other from rust. There was nothing left of the heads of the manifold nuts to get a wrench around. When Ford designed these engines to go over 250K, they did not consider the longevity of these components. EXOr's die grinder idea is sort of the way I removed everything.
I went out and bought a remote cable drive for my Dremel tool. This way, there was no need to remove any trans or motor mounts. Removing the front wheels to work though the wheel wells, as well as underneath, was all that was needed as with the cable drive, you can get you hand in there and grind away all the manifold studs. The cut off wheels for the Dremel are a little pricey to keep replacing, as they are fragile and will break off from time to time, but well worth it compared to struggling with even a small air cut off wheel, which I was able to use on a few. For this type of job, it's even worth sacrificing, burning out a Dremel, compared to what a mechanic might charge, although I never burned out mine.
When the manifolds are off, enough of the stud is left in the aluminum head to draw them out with a small Visegrip, after soaking overnight in PB Blaster. I don't remember, because it was a couple of summers ago, but I may have used double jam nuts to remove a few. When I replaced with the new manifolds, I thought it would be nice to use at least stainless nuts for the next guy, but after recently replacing the truck @210k with a low mileage '05, it probably will never be done again. Knowing that back then, I just used a NAPA stud and nut manifold kit for that engine. I installed them with plenty of antisieze and then covered all the nuts, including the down pipe, with orange hi-temp RTV, so that if there is a next guy to come along that needs to remove them, he has a fighting chance and won't have to go through this lengthy, but effective procedure.
