With resto mod's one should build a harness from scratch. Butchering in factory harness usually results in nothing but problems. I have had many an auction car come through with multiple issues.
American Autowire is my go to on the start of the project. Usually using therir Hiway 21 kit and build off of that. Painless harnesses are 💩 but they have offered harnesses for the ECM's etc that have been pretty good.
one needs to understand basic DC electronics and MOST importantly that there are different terminals and specific crimpers for those terminals. Scotch lok and butt splice connectors along with a lack of knowledge is where Bubba fails .
here's a few examples

I worked at FCA debugging prototype vehicle electrical issues for 10 years. This was after 30 years of flat rate tech work at both independent shops and Dealerships. Learned a bunch and became pretty proficient at it before retiring. What you are talking about could be fairly simple. Or near impossible. Depends on how new you are talking about. The last 5 years or so would be a can of worms. There’s way more to it than just running the wires. Intersection points and harness lengths can drive Can Bus crazy. Wire routing next to high amp circuits and multiple ground loops can send you for a loop. Many modules need messages with start and shut down times in a given order. Module A needs message to start before module B and so on. These are things very few in the aftermarket know much if anything about. Now when using an aftermarket controller it may not be anywhere near as sensitive. I’ve lived it. It can be frustrating and extremely time consuming. Example. You want to start the engine. The RF hub receives a signal from the FOB. The BCM and the KIN (key button) compare codes. If they match the KIN signal to the BCM is received and messages are sent to the ABS for brake pedal info. Also to the TCM for Park signal. Now the PCM looks at those and gives the OK to crank. The ECM looks for TAC (throttle) crank, cam signals. Then signals to prime the fuel pump and spin the starter. If the PCM sees everything correct it’ll send injector pulse and drive the coils. This is just a rough outline. There is actually many more parameters to just start and idle.
Doug

Meanwhile, a microprocessor is deciding whether it's okay to turn off the dome light.

For $500 you can do it yourself

https://www.hptuners.com/vehicles/stellantis-tuning/

While on this subject is there a company that can tweak an existing factory tune ?

It’s not just the PCM. It’s the BCM, TCM, and ABS as well. A late model trans and engine swap is much friendlier with aftermarket controllers and harness. Heck if you build a late model Challenger, Charger, etc.. You have to source a separate controller just to run the windows up and down if not using a factory harness and BCM.
Doug