Any exhaust shop will be able to mod the pipes and install the new mufflers for not very much money. If you have a welder and sawzall/cutter and some skillz then all it takes is time in your driveway.
Also Magnaflows are a straight through muffler, just offset inlet/outlet and one of the best mufflers if not THE best one available for these cars. I'm not even talking about sound I'm just going from a strict construction/quality/material standpoint although I do think they sound amazing.
2000 Mustang GT Steeda build #48. Bolt ons, suspension, Novi 2000.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.