I'm working on my Y-pipe to cat inlet flange too (not able to get the top two bolts off yet - muffler shop says they can't burn them off without damaging the flange), so am interested in this thread.
Thoughts . . .
Possibly taking a flat file to the mating surfaces (if you haven't already) might help? Also, if you can get the cat completely off, the belt sander/machining route?
I'm also wondering if one took some thick copper grounding wire (sheathing stripped off) and made a wind or two of this around the outside of the pipe holes of the flange but inside the bolts, whether this might make a copper crush-fit seal? Perhaps there are appropriately sized copper rings available at a good hardware store?
FYI - I just bought an older car, with an overhead cam engine and deeply recessed spark plugs, that had recently had the valve cover gasket replaced. When I pulled the spark plugs, there was some rubbery black silicone on the electrode, inside the combustion chamber (obviously the guy replaced the plugs while silicone was still oozing out from the gasket, and got goop smeared on the end of the plug). What astounded me was that the silicone was still solidly clinging to the metal of the plug, and was still completely rubbery! I don't know exactly what brand/type this stuff was, but it sure stands up to heat.
One other thought, perhaps use of metal epoxy, but using about half of the proper amount of hardener. This might give a tough, heat resistant fill, but still retain enough flexibility to not crack and blow out?
Kunar, please keep this thread updated with your progress, and if you find a solution.
CraigK
P.S. I will never again use regular bolts and nuts on exhaust systems. For a couple of bucks extra, I use only stainless steel hardware. Bolts are shiny, clean and easy to remove many years later.