MarylandGuy: A lot of the fixes suggested are "KISS" type and should be considered before getting too clever. You are going to be okay because you instinctively went to modifying the part to fit the car not vice versa. Modifying the part usually means you can go back if something doesn't fit/work
I have a lowered Thunder Speedster. For future reference, I found the VS lowered bus setup worked well for me. It tucks up underneath, single out pipe runs parallel to the muffler. There still may be a picture on the Aircooled site. I'm a VS fan, I like their stuff well made with good hardware.
Keep the shiny side up, and stay between the ditches.