So I think I've found another issue and I think it's probably the main cause of the loud noise and reduction in power. It looks like the threaded hole in one of my heads (originally for the SAI manifold injector) stripped out and I've lost the plug. So the broken head stud I found earlier probably wasn't the root cause. It doesn't change my plan to change out the exhaust head studs, just adds some scope to the head work.