Not trying to be a smart ass- but have you pressed on it to see if it will push back in? There's a series of clips that attach the cover. You can pull the trunk carpet back and see down from the inside if any are broken or missing.
My passenger side has a slight wave to it. Similar to but not...
Used an Aisin timing belt change setup (new timing belt, water pump and tensioner on my old Honda Civic.) The Aisin stuff was oem replacement and never gave me an issue. Quality and price were both on point. That was circa 2016.
Somebody on here was having a hell of a time with the computer after doing gears. I think he eventually threw in the towel and put the 3.55s back in.
Any driveshaft upgrades or additional stuff to make the gears play nice? Driveline vibrations? I did 4.10s in my old 04 IRS and it vibrated so...
If they said it was normal, then what did they say it was?
But to answer your first question, no. This is not where questions for a '24 go. M7G would be the place.
I think it sounds like a really pissed off 4 banger, if I'm being honest. Which isn't even in the same universe as a '350. I'll pray for you in the mean time about the valves. That's weird.
This thread has all the parts and bolts you'll need. Best thread on here for this mod.
https://www.mustang6g.com/forums/threads/pp-strut-tower-brace-kit-cowl-extension-lower-k-brace-install-guide.100800/
My guess would be gear backlash in the rear. Mine has done it since new and can happen in just about any gear if you hit the clutch 'wrong'.
Used to have an IRS in my 04 Mach 1 that did it also. It was a common thing on the Terminators. My friends 04 Cobra does it. If that's what it is, you'll...