Those manifold to pipe studs are a bear. One of the nuts rounded off on me when I was installing BBK ceramic coated shorties. I had to use an angle grinder to cut the stud. [Don't use anything but a six-point impact socket on those nuts.] The head to manifold studs can also be a pain. A six-point socket might remove them, but the 12-point will ordinarily round them off. If the shop broke or rounded off the stud you might be able to jam two nuts together on the stud, and turn it off with the inside nut. That worked fairly well for me.
Once I had the manifolds out, the hardest part was cleaning the gasket surface. A Scotchbrite™ pad on an oscillating tool worked great.
I like my shorties. Hard to see any change in mileage or power, but the car runs great even in Michigan's winter. I also like that they keep under-hood temperatures down.
The ceramic coated shorties were expensive, but they might be cheaper for you at this point. Sorry to hear you had trouble with the shop.