I have seen some cases where they shot clear over the original to protect it. It would require light wet sanding.

It looks to me to be a kind of coating that isn't doing well with gas sitting on it.

I'm not sure you really would. It also depends what all you use your truck for. If you do much towing, it will show in harder to get going. That said, My 88 F250 has those gears, 351W and 5 speed, and it never got the greatest fuel mileage...

I did see they are available new online. LMC Truck has them, as well as many other sources. https://www.lmctruck.com/body-components/bed-tailgate/fd-1987-96-styleside-and-flareside-tailgate-parts

Headlights have a breaker which I believe is integral to the switch.

I would think you should be able to find them in salvage yards fairly easily.

Without viewing the video, I'm just going to throw out that it may well just be a shift solenoid failed. Traditionally, the clutch packs were controlled by hydraulic pressure alone, now it is all electronic solenoids controlling the hydraulic...

Sounds like the ECM isn't quite right, the calibrations have to be correct. Unfortunately they are not all made equal, it has to be the right program or it will exhibit behaviors as you have seen.