2018 MT82 to T56 Magnum XL issues

[happysem]

Long post but I'm trying to be thorough so bear with me, having massive problems with my 2018 GT MT82 to T56 Magnum XL swap.
2018 Mustang GT, turbo car, bought from dealer so I have no idea whats done to it. (here's your sign...)
I assume it has an aftermarket tune, it ran clean when I test drove and the first two days driving it. Low boost due to boost leak, but I'll fix that later when I can actually drive the car.
Did 1 WOT shift 3-4 and broke the transmission.
Car ran perfect even with a likely bent 3/4 shift fork. Drove it for a couple weeks just skipping those gears. Had NONE of the issues below.

Modern Driveline T56 swap kit, Bowler all in one harness. Did not have revmatching before, and this transmission does not support it.
All I did was swap the transmission, clean air filter, and put in new spark plugs.
Now the car is very upset.


Multiple issues:
Car will not start - push button, flashes green no solid, "push clutch to start" message. Checked switch its fine, jumped connection, new switch, no changes. Only way to start is with a remote switch I have wired to the starter.
Crank Relearn won't work - have the code for the relearn, tried it via HPTuners, Bama hand held, and Ford ProCal, says it is complete/successful but code stays. Car runs a bit worse than before, but not a limp mode. Just a bit off.
Hood open switch - says hood is open no matter what, same with clutch switch, cleaned, tested, swapped, no change. Also makes alarm go off randomly, wipers/fluid to not work ever.
BRAKE light - e-brake light switch stays on, think its related to hood switch telling me to pull over and fix it.
AIRBAG light - on all the time now.
Wrench light - on all the time now.
My modes disabled - not sure.
Service advance track, traction control light intermittent, probably related to above issues.
Driver headlight no longer works.
Back up camera/parking beeps don't work - Bowler said this unfortunately won't work with my car. Reverse light and reverse lock out work correctly.

Some people say this swap works with 2018's, others say it doesn't. I've been all over the internet, called multiple shops, and talked to Ford.
Can't get a straight answer and not sure where to go next.
Bowler and Modern Driveline think I "may" need a new tune? I feel like thats a long shot.
I double checked all the fuses, relays that I could think of, double checked wiring for trans, confirmed with Bowler it is good (speedo works, but cruise still doesn't)
Ford wants nearly $1200 just to look at it for diag since it has mods.

I'd be very unlucky for the BCM/can bus system to all of a sudden break while swapping the trans, but I don't know at this point.

Anyone with positive confirmation that this swap works in 2018s? I know theres a ton of issues with 2019+ cars.
Any ideas?

[veeefour]

Did you ever used another tuner? Always on the stock file?

Switchin off the rev match is not an isse. We swaped the stock 2020 manual to 10r80 everything is possible.

[skylinedan]

Check that wire harness I've heard of people having all kinds of issues, and it turned out the wire harness had some terminals in the wrong spots.