I get the frustration with tuning issues. Since you’ve got a 5” exhaust and blocked EGR, it might be worth checking out an LB7 EGR delete kit, which can help improve exhaust flow and reduce restrictions. Here’s a good option I’ve come across: LB7 EGR Delete Kit.
As for the FlashScan issue...
That’s awesome you got your first truck back! With 270k miles, it’s definitely earned some TLC. A level kit and fresh shoes will give it a nice facelift. Can’t wait to see the pics—good luck with the build!
From everything I’ve read and experienced, transitioning from round to oval and back to round in the downpipe shouldn’t cause any issues, as long as the cross-sectional area stays consistent. Oval exhausts are actually pretty common in tight-fit setups, and they don’t create noticeable...