The issue is if the guys that did your swap didnt document what they did, the wiring routing and even how they pinned connectors, this is going to be next to impossible to troubleshoot over the internet. Its a hands on thing.
In short (Pun intended), Short circuits and too many amps blow fuses, usually the too many amps is a result of a short, but it can also be cause by too small of wire being used when wiring in components, too much resistance in a circuit will also blow a fuse. Im sure you know this, just thinking out loud.
As a technician, 8/10 wiring issues I find and repair can be found visually. The other 2/10 can be found with a multimeter turned to the Ohms setting.
Connect your ground lead to a known good ground, on 80s I just hook on the battery since i have very long test leads for my meter. Unplug your engine computer, with the key off of course, and put your red lead on each pin on the engine harness connectors. A few of them will probably have continuity to ground, this is where it will be critical to have a wiring schematic of your truck and of your engine, both can be found online with a little research. The idea is were looking for pins that have connection to ground that should not. Some of these will be false positive results, for example, a fuel injector solenoid will show a "short", in terms of having continuity to ground.
If you find a pin that is grounded, it will be helpful to know which component or location that wire is running to. So say you find a pin for you oil pressure sensor is grounded, it would then be necessary to unplug the sensor and test the continuity of each wire to that sensor, from the big connector at the ecu to the sensor. Like I say, some wires should be ground, others should not. This can get confusing, time consuming and frustrating, because in order to troubleshoot these types of issues, I need to know what I am looking for on each wire.
Another common test would be to connect your red lead to a connector, any connector in which you expect the circuit is compromised, lets say the O2 sensor is throwing a code you would unplug the sensor and put either one of your test leads on one wire, youd then go to the big connector on the ecu and test continuity on EVERY pin, in a good harness you would expect to find that pin to only have continuity to one pin on the ecu. It is possible for a wire to be shorted to the frame, its also possible to have a wire shorted within a wiring loom, to another wire.
If you can share wiring schematics I can look through it and help you track down some items.
The windows opening and what not leads me to believe you have a bad window module in one of the doors, either the drivers or the door that the window opened on, but the codes for your modules kind of blow that theory out of the water.
Do you know if the company that did your swap utilized the factory fuse panel? Can you see any of the wiring harnesses resting on exhaust components or the cylinder heads? Does anywhere in the harness look melted, pinched, crushed or chafed from abrasion? I would begin by running my hands along all the harnesses you can reach and feel for physical damage. You have enough going on I suspect the power supply to your modules is compromised, likely the fuse panel is melted or damaged, or you have an area that is significantly damaged somewhere on the wiring harnesses under the dash or in the engine bay.
Very long winded reply I apologize, but happy to help if you want to dig into it.
