(edit- I may be confused on which set of manifolds you tried to separate, but...)
Leave them together then. It might be a bear of a task to obtain correct Alignment, seal, and to not break the bolts when installing your old manifold if you do take them apart.
I believe we (the machine shop) had to machine my engine block to get my manifolds to seal perfectly (on re-install). The machinist/engine builder said, "I wish you'd have just left them together."
Handle the carb issue first; I am not experienced enough to know if a leak on your exhaust manifold would cause the engine issues you're having-- Good Luck!
Brad
