Lowering with 2-1/2" exhaust

I recently instaled a MAC 2-1/2" cat back exhaust on my 03 Mustang GT. After I installed the exhaust on my own, it was hitting the rear axle so I took it to a local mustang performance shop where they adjusted it so that it no longer hits the axle. The gentleman that did the work said that he had to adjust it and flaten out part of the pipe because it seemed like it was a little to long. Her is my problem, he said it is fine now but if I wanted to lower the car that I may have a problem. Has anyone had this same problem and if so how did you solve it because I would like to lower the car but I don't want to do it if it is going to cause the exhaust to hit the axle or suspension.

I have an '01 GT with a MAC cat-back that is lowered 2" and have no problems with the exhaust scraping and I had to modify my exhaust in a similar fashion as you.