So about 2 weeks ago I got new wheels and replaced my wheel hub due to a stud backing off and stripping out the splines, my 98 had been sitting in my shop for about a month while i waited for parts and to press the new wheel bearing and hub in. I went and picked up some Work Wheels and was intalling them and the knuckle back into my car on the passenger side, I had a buddy over who wanted to go to a car meet so he was rushing me. He came up with the idea to take the battery out of my Mazda B2600 minitruck and put it in my car to start it since my battery was dead from sitting and he wanted to leave. He went and grabbed the battery and put it in, i hooked it up in a rush because we were trying to leave and accidentally reversed the polarity for roughly 45-60 seconds on the battery. My horn wouldnt stop going off during that period of time and my car didnt start afterwards, i looked on forums and found some people who have made that same exact (dumb) mistake and replaced all of the fuses and relays people had suggested that could have blown. My car started up no issue with a jump and i had all my interior lights and dash lights back. The ECM isnt fried clearly because it still reads my knock sensor code and so i sent it and drove 45 mins to another meet, while i was at the car meet my car was running with the interior lights on, a bluetooth transmitter plugged into the front cigarette lighter port and a little purple flashball plugged into the rear drivers side lighter port ( i wanted all my cool purple lights to be on during the car meet). Roughly 30 minutes into the drive back home my radio started cutting in and out and my dash lights dimmed along with the battery light turning on. I took the nearest exit and as i pulled off the highway my car bogged down and lost all power and lights. I had a buddy come jump me and it started no issue but diidnt make it 300 feet until it died on me again. I got it towed back to my shop and replaced the alternator since that was the only thing left i could think of. Today i finished the installation and jumped it, started no issue and i let it charge off of the jumpers but as soon as i removed them from the battery it idled for roughly 45 seconds before bogging down and losing all power again. I am now letting my battery trickle charger overnight but ive read the alternator wires could be fried or something along those lines. Any help is appreciated

 

I looked into the original owner of my car about 20 years ago the gal did the same thing reverse polarity jump start on a dead battery, the dealership ended up flashing the ecu or re-mapped it or whatever they did. The ecu ended up being fine, The event did however blow fuses, and there was one wire that got damaged that they had to replace though they did not specify exactly which one it was. So you reading wires could be fried is a correct assessment, it's kind of tedious work and tracing and checking wires but could very well be what is causing the problem.

 

The ECM is seldom to fail when reversed the polarity is applied due to the reason that reverse voltage protection circuit is build in. So are most other electronics units. The protection circuits pass through extra currents and related fuses are blown. Other than the 120A alternator fuse, it is the often case that some other fuses are blown. You need to check those fuses one by one and replace blown ones.

What I worry about is the reversed time for 45-60 seconds. Longer the time more serious are damages to components including the harness.