Nightmare Problems With Brakes on 2007 Prius

So my auxiliary battery started dying and I had to jump start it when it was dead. One dark morning I reversed the cables on my wife's car when jumping it. The portion on the Prius that I had hooked up the cables to started glowing. I unhooked them, and when I got inside my car I noticed several warning lights on (ABS, etc). Once I got the car started I drove to work, but the brakes were no longer working correctly, and if I hit them hard they would lock up and I would skid, with tons of white smoke from the tires. I took the car to Toyota, but they wanted $550 to replace the auxiliary battery and run a diagnosis. They said they could not run any computer tests as the car's auxiliary batter was too low.
So I ordered the battery off of Amazon. In the meantime, the brakes wore down to metal on metal on the front driver's side. I took the car to Firestone and they wanted $850 to replace the pad, rotor, and caliber, which they said was stuck. I then put the new auxiliary battery in the car myself (it was relatively easy) and took it to Toyota. Initially I was told it would be a $250 charge to run a diagnosis. They then said the ABS relay needed to be replaced for a reasonable $68.45. After waiting two days for the part to come in, I then get informed that the skid control ECU needs to be replaced, at a cost of $1,984.44, at which point they will "recheck as necessary with diagnosis." After doing some googling, there is some indication that the problem might not be the skid control ECU. I don't want to pay $2,300 and then have them say other things are wrong. Does anyone have any thoughts on this?

 

Thanks Patrick and PriusCamper. Yes, my car was able to start after I jumped it incorrectly, and it ran well until the front left break was metal to metal (other than going into a full skid if I hit the breaks hard...I relied on that "B" selection on the transmission to slow it down). I did tell the Toyota dealer about how this all happened, so I hope they considered the fuses/inverter possibility. I know I must look like an idiot, but in my defense, the "-" sign on my wife's battery has a small scratch on it, perpendicular to the negative sign, making it look like a positive sign. It was dark when I was doing it and I didn't catch it. Apparently this will be a very, very costly mistake.

 

MPG remained around 40 mpg. I did unfortunately drive it for awhile, as I had to order a battery, and I took it in multiple times to various places. The people at Firestone (who did not know what they were doing) said the car was only braking using the front driver's side brakes. There were a few other issues...the driver's side electric window button no longer has the function where you can push it once and have it automatically go down all the way, and the disc changer beeps several times when the car starts and does not work (I cannot even eject the discs). I'm just worried that I'll pay $2,300 and then they'll tell me it's not the skid control ECU after all.