Electrical issues after car caught fire?

Hello, that sounds like quite the event. It sounds like you powered up the fuel pump yourself with an aux power source. And at the fuel pump relay location how many of the pins have power with the key on?
And what tools do you have, scan tool, multimeter etc.? Does the Fuel pump come on with the Hazard switch on now with it hooked up and a new fuse?

https://www.2carpros.com/articles/how-to-check-wiring

https://www.2carpros.com/articles/how-to-check-an-electrical-relay-and-wiring-control-circuit

Here are all the diagrams you should need; it sounds like power is missing from one or more Fusible links. They are marked in the Fuse Box diagrams, although I don't know what type of fusible links they use in this model, they may have a plastic cover over them. The A/T power relay in under the driver side dash as you can see in diagrams 6, 7. Also when checking the Fuel pump, never power it up dry, that will burn a fuel pump out quick. So only run the pump while in the tank.

So, you're not getting full voltage back to the fuel pump, can you check it with a multimeter and see how much voltage you're getting. And when you checked the fuel pump connector did you put the test light in place of the fuel pump at the connector, using the fuel pumps ground to ground the test light or did you ground at a different location?
With a fire like this, there could be any number of locations where circuits shorted out, even shorting power right through the PCM.
And does the Start fuse have a number with it, most of these wiring diagrams are only showing numbers for fuses.
Did you replace all the relays and fuse boxes in the engine compartment after this fire?
What does come on with the key at this point? Does it crank over, and do you have spark?
Here is the PCM connector pinout, to verify that power and grounds are good for the PCM, also check that there are two 5volt References.
Pin 67 is the wire that the PCM grounds to activate the Engine control relay and pin 69 is grounded to activate the Fuel Pump relay.

So, you've got a low voltage issue on the feed from the fuel pump relay to the fuel pump connector. It looks like there are two connectors on the fuel pump positive wire, EM02 and MM02 with a multipurpose check connector in between those two connectors, I'll see if I can locate both of those connectors. There are supposed to be photos of them as well.
Both the connectors are down on the lower drive side. Connector EM02 looks to be for the Passenger compartment junction block. So, checking the MM02 connector behind the driver side left kick panel for a full 12volts will be faster since it's further down the circuit towards the pump.

Okay, let us know what you find. It might be that there is a ground to the engine block or body that got overheated and has high resistance now.

Restore any grounds that are missing that were there before the fire. You can even use some jumper cables to temporarily run some grounds to the intake and then to the battery negative. Did you see what the voltage level is at that connector behind the left kick panel? If you still have low voltage at that connector, then move back farther up the circuit to the next connector, that is the passenger fuse box connector. But using jumper cables to run quick grounds to everything will tell you right away if it's a grounding issue or not. Definitely hook one up to the intake on a metal bracket for testing purposes.

The TCM relay is always grounded, it's a power fed relay, so the PCM supplies power to the relay to activate it. The PCM controls the transmission and engine in this vehicle. What do you mean by harvested voltage for the fuel pump? Did you find a location where there was a bad connection? You should be okay with the new PCM, as long as it's programmed to the VIN, if the fire was enough to melt the front-end suspension, I'd be concerned about the old PCM as well, I know they are not located in the great place in the engine compartment on these vehicles. The new PCM should be clear of codes unless it's seeing any circuit faults when you turn the key On. Other faults it will detect when the vehicle is running again, so we'll deal with those once it's back up and running. Can you get a voltage reading at the fuel pump connector with a meter, so we know how much voltage is back there?

Okay, I'm sure that if the harness was melted some power wires shorted to grounds, there was probably multiple shorted circuits. But let me know tomorrow what the fuel pump feed is reading.

Okay. Yeah, without a battery being at least 12.6volts, and can hold voltage when loaded such as when cranking, that needs to be taken care of first.

Okay, the EM02 connector comes directly from the Fuel Pump relay, the control side of the relay is powered up after the Engine Control Relay is powered up, the PCM is responsible for grounding both of them. The engine compartment relay and fuse box have the Fusible Link 20amp the provides power to both relays on the load side. So, it can be either you have a bad fuel pump relay, a bad Engine control relay, or some issue with the control sides of these relays. If you pull out the Fuel pump relay there should be power on 2 of the pins in that location with the key on, there should be power on 1 pin of the Fuel pump relay location all the time, as well as 2 of the Engine Control relay pin location all the time. So, if you are missing any of those 12v feeds to those relays, then there might be some corroded pins on the underside of the relay/fuse panel.
In the engine compartment they tend to corrode and break off due to exposure to the elements.
If the Engine Control Relay is not working, power will be missing at the SNSR Fuse 10amp and INJ Fuse 15amp. Those fuses feed power to the Injectors and ignition coils. So, checking power at those fuses will tell you right away if the Engine Control relay is at least sending power to those fuses. You can see there is a joint connector between the 2 relays, so there could be an issue in that fuse box. But check for power at 2 pins of the Fuel pump relay with the key on.
Also check the Engine control relay pins for power 2 of them, hot at all times.