I had mine Ziebarted (I live squarely in the rust belt), and pulled the liners when I had it done so they could spray that part of the bed. I've pulled them each year, and have noticed no issues at all - no wear on the rustproofing from the liners and no noticeable issues of any sort.
Bought mine with 1640 miles on it, just turned 75K. Got another year of payments, and not looking for another car/truck payment for a while, so I'll see how long this thing will last me.
I'm running the same size, but I did a 1.5" level shortly after getting the truck, with no difference in ride quality over non-leveled. After the stock Goodyears wore out, I replaced them w/ Cooper Discoverers in 276/65R18. Only a couple of pounds heavier than stock, so very little hit to gas mileage, and still rides good. WORLD of difference in traction on wet roads and light mud over the stock tires.
I've got one as well. 4 years now, and holding up great. I put a little bit of white lithium grease on the part that goes into the lock a couple of times a year, and not a single issue.
Yours is the first time I've heard of a problem w/ the app. Sorry for your issue; I'd be upset too if it didn't work correctly for me. I've used an iPhone SE and my current Galaxy S9+ and have no issues with either. With the knowledge above, I'm at a loss as to what you can try next.
I'll admit it! Messing w/ a tune scares the sh!t out of me. Bolting on a superchager/turbo/intake and carb, fine. Tunes? Clueless. All I know is that w/ my truck, once I hit 100k, I want to tune it to improve trans shift, and overall performance. Just make it run better with out spending $1000. But after reading through this thread, I'm more confused than ever (not that it takes a lot to confuse me...).
Mine runs no differently w/ the flapper bolted open. Only difference I've noticed is a little bit louder at startup when I auto-start it in the barn, and a SLIGHT helicopter sound under light acceleration in V4 mode.