Well, I got the rig back today nearly two weeks later. I got a new rear floorboard and they applied a insulation barrier to the underside of the floor. Sure hope this works...
They ran diagnostics from data pulled from the ECM...normal. They pulled plugs (installed new plugs) and the plugs were actually running a bit rich, which surprised me being fuel injected, newer FI stuff usually runs lean...normal. Nowhere did they find any reason for it to burn a hole in the floor.
I looked under and there is plenty of clearance between the pipe and the floor and lots of shielding.
Time will tell...sure hope it doesn't happen again.