I think my 390 has a somewhat similar setup. When changing a flang gasket I found a crack in the manifold. I salvaged a good replacement manifold. As far as the studs, i replaced with all new grade 8 studs and hardware. The parts store had quite a selection but all were either shorter or longer than what I needed. I got the longer studs and ground them down to the length I needed. I then applied a bit of High temp locktite and snugged them up.

This seemed to be the best way to replicate what Ford did on a dime. Hope this might help.