Since you have an MTX there is no flex pipe. The nuts on your Y-Pipe to Catback connection have tab stops, and if they've already rotated against the ****** no amount of torque is going to move them without breaking something. i.e., don't turn the nuts, turn the bolts (maybe you are, but I couldn't be certain from your description).
So turning the bolts should at least rotate the nuts with the tab stops back and forth. If you can rotate the nut against the tab stop and then it's stuck if you try to go furhter, then soak those dudes with your favorite penetrating oil. If that doesn't help a propane torch against the nut for a little bit might help (the usual disclaimers here about being mucho, mucho careful).
If you can't even get the nuts to turn a half-turn either way until the tab stops hit something by turning the bolt, then penetrating oil everywhere until you can at least get the bolts to turn the nuts. Once you get that far then if you're lucky you can get the nuts off by turning the bolts. If not, see the previous paragraph. wink
Hope that helps a little bit.