This is where the entire industry is going.
Some manufacturers are VERY bad about this. Like Audi and Tesla.
Oh you want heated seats? You have to pay a monthly subscription to turn them on.
Toyo 255s all day. Especially since you are looking at 255/75 a C rated tire.
I went from the stock Grabbers to the 255/80/17 Toyo AT3s. They are excellent.
I'm very happy with my Ranger.
I'd go with the Ford Performance tune if you want zero warranty issues, or the Livernois Motorsports tune if you are willing to take some risk with the warranty.
OP is getting a ton of non-answers.
OP check out the ROW rear leafs, Tremor leafs, or the OME set.
All of them will smooth out your ride.
I wouldn't mess with shortening the bump stop.
You mentioned paint defects. I'd inspect for tape lines, over spray, check the fender bolts, bolts in general for signs of disassembly.
If you are generally worried, maybe a body shop would be willing to check.
EDIT: Carfax wouldn't pick up a transit repair, since those are always done...
I put your problem in bold.
Anticipate light changes more with braking and acceleration.
Creep instead of hitting the throttle to pull forward in bumper to bumper, aka just let off the brake.