It's kinda hard to trouble shoot this without seeing the car, but I'll give it a shot...
Did you try turning the flange that's on the header? I have MAC unequ headers and I can turn mine. I also have a set of BBK long tubes that are waiting to be stuffed in. I can't remember if they turn or not
It's been a while since I had the stock H-pipe. I thought those flanges turned as well...
Sounds like I ain't being much help.....
If that didn't work, I would try to "bend" the H-pipe to see if it will fit. If I couldn't do that... then I would just run open header