Engine light on

First off, my car has manual doors, locks and clutch. I have never had a days problem out of my car until now. In November rats chewed eleven wires on the body harness. The location was right at the engine firewall area. It was a tight spot and hard to find. The insurance wanted to total the vehicle over the repair cost. Since my car has been so good, I could not see taking that route. I am also, a widow and female with very little money. So, I got my tools and went to work on it. The car had no start, no crank.
I had to remove a fair bit of electrical including the fuse box, PCM and related wiring to get to the wire harness to work. I managed to splice, solder and heat shrink all the chewed wires. That allowed me to get the car up and running. Though my alternator was not charging. At that point I order my part and took it took a shop that was once very reliable. The day I took the vehicle to the shop, at the shop and when I came back to the shop, the car was still able to show codes via the OBDII port. On the day I was to pick up my car, I noticed the check engine light come on. I did a fast scan and showed my car was not charging. I took it back to the shop he tested and agreed. He said he missed something. Nine days past and he had not fixed my car. On the day I came to get it he said that it was not charging and the computer was not working anymore. I was quite upset and drove the car to a new garage on its battery. The problem turned out to be that the generator wire was not tightened onto the starter. The new shop also showed me damage to where the other shop had broken plastic areas looking for wiring issues. The new shop also cannot tell me why the car is not communicating with the PCM. They checked to data port with a meter and all the metal prongs inside the connector showed to be working. I brought it home and the check engine light is on, and occasionally it seems to miss a bit. Before it went to the first garage this was not an issue ran great. What are your thoughts on what I should do next? I am sort of lost at the moment with it. I appreciate your help in advance. Thank you.