I went through my own exhaust hell today. I too replaced the manifold to downpipe gasket. Did it mostly from the top (God I love ratcheting wrenches) Managed to cut my thumb on the gasket itself when I was reseating the downpipe. The new gasket fixed that leak there, but I knew the resonator was leaking anyway.
I decided to go to town and buy the stuff I needed to replace the resonator. Got me a Thrush glasspack, a flange, an adapter, and a few clamps. Went to my uncle's where we proceeded to weld the flange to the glasspack. I figured out where I was going to cut the factory catback, and then decided to cut the studs on the factory resonator since the nuts were not going to come off by normal methods. Once both studs were cut I smacked it once with a hammer and it separated, but I also noticed the flange on my ZZP downpipe was essentially breaking off the downpipe.
I proceeded to pull the downpipe out. This time since the car was already jacked way up I decided to take the nuts off from the underside. I got both broke loose and then took the drivers side one off. I was taking the passenger side nut off and felt the downpipe putting pressure on the nut, so I went to put my hand up to hold the downpipe and the nut must have hit its last thread because the downpipe fell and smacked me right in the head. It didn't necessarily hurt that bad, but as I got ready to roll out from under the car I felt blood running down my face.
Got that cleaned up and put a band aid on to keep from bleeding everywhere then we welded the flange back to the downpipe as best we could. I put the downpipe back in, I fitted the new resonator assembly and new gasket and bolted everything up. Fired the car up and immediately knew something was wrong. First when I put the downpipe back on I didn't realize the gasket fell off one stud, so it came off again, reseated the gasket, and fired it up again.
Still loud, so I crawled under the car and it was leaking at the flange. My uncle was getting cranky, and I was too so I decided to just clean up and see what I could get in town.
To wind up an already too long of story, I tore back into it after a run to town. The flange on the downpipe was warped to hell and back. After I pulled it back out again I set it flat and tried to hammer it flatter. I used some muffler sealer to try to build up the flange a little. It got dark on me so I called it a day. Got invited to dinner a little later, and since we were already going to be in town I got to stop at WalMart and get some quick steel which I will use to try to level the flange even more tomorrow.