Good job.
Some of the under dash harness is for a factory towing controller for trailer brakes and signals wiring.
The harness may also contain provision for air bag suspension controls for trucks with added dealership installed features.
You may not need them for anything if your truck was not the loaded version.
The glove box will show you the codes for the options you may or may not have.
Chances are the voltages screwed up the fly back zener diodes within the cotrol switches in the overhead systems.
One sure way to know if you have power is by pulling the overhead control panels and testing the tiny light-bulbs, if they do not light up when you turn on the headlights or interior lighting.
If the tiny bulbs are good (ie: they have continuity when tested with an ohm meter when removed from the control panels), and they light up with separate 12v testing power, then your controllers no longer have power and ground. The switch panels are for sale on AZ if yours is blown.
Now you know why buying a used unit from ebat can be a rip off, if they are selling a blown unity for $65.00 or around half of what a new replacement costs.
Voltage spikes from the alarm could have ruined the expensive sensitive switch controllers, by allowing back flow of voltage through the ground circuits and destroying the single direction zener/resistor circuits designed to limit fly back effect. Several systems can be effected, making diagnostic very difficult.
You are correct presuming the relays also have a resistor for fly back and could also be blown, however, if other fly back's are ruined, swapping relays may not fix the issue... You see how this can be running in circles?
Check all your grounds and fuses before you mess with anything. Verify the lights work and if they are blown bulbs, if they do not.
If this does not fix anything and your controller(s) still malfunctioning:
It is possible your head light switch is ruined and causing the other systems to mal-function too.
Everything is switched in the most confusing way through the headlights switch... (don't argue with this logic... it is a fact).
The headlights and wiper circuits are very difficult to explain to a non-automotive electrician. The wiring diagram will confuse you for months if you cannot understand the methods the engineers used and the math required to make it a dealership repair, (***all on purpose, so when it breaks you buy a new truck after your local mechanic cannot find the issue to fix it).
When you add a system disrupt-er like the alarm you cross connect the sensitive confusing voltage systems GM has designed.
You're lucky if your wiper control module is not blown or the headlights switch has not burned up the circuit which routs power the controllers you are having issues with.
Verify the wiring colors at those black factory connectors and I'll bet you find they are for factory trailer brakes, air bag suspension, the more advanced radio / GPS audio video system, etc... may not not be your issue. Search the web for the super expensive options packages this truck could have come with, rear A/C and heater, heated seats, supreme audio, full trailer controls... before you jump to conclusions what they do.
Does your cluster work correctly now and do you still have a working battery after 3-4 days of sitting without running?
The diode in your dash is what I am most concerned with... $350 is a lot of money.
It it's blown and you do not find the other issues, it can blow a new rebuilt replacement if all the possible fly-back issues are not found and repaired...
Good luck.