You need to get under there and loosen the header bolts. Cut off those hangers. You don't really need them. If you're worried about not having them, just get some generic, adjustable replacements. Use a jack to support the H-pipe as high as you can and then tighten the header bolts. That should lock the h-pipe in a higher position.
If you only clamped the Flowmasters on with the u-bolts, loosen the u-bolts and rotate the muffler until it is flat. Make sure that the tail pipe doesn't get repositioned too close to the fuel lines when you do this. You may need to loosen the clamps on both sides of the muffler to make sure you have full adjustability.
If you had them welded, there's not much you can do about the mufflers.
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