I clamp the studs in my shop vise @ turn the nut with a box end wrench; if the nuts still wont unscrew I heat them to orange with my oxy0acetylene torch. I then install the studs first, using antiseize compound of course, and put the nuts on also with antiseize. I doubt it matters much whether they are left on the stud or not. The problem with using stainless steel is that you shouldnt use stainless steel studs, and stainless nuts. They dont like to live together. Stainless studs in an aluminum threaded hole can come out taking some aluminum with them from the head; a term called "galling". With the alternator out isnt it possible to get s deep socket onto the nut on the extreme left of the exhaust manifold? I dont think I have to remove the accessory bracket, though I did remove it most of the times I was going to hoist an engine/transmission up and out. I hope you are using 6 point sockets on those exhaust manifold nuts/studs.