[amitmishra4]

So by searching the amazing interweb, I found a couple answers - as far as the one touch function for the windows, they need to be retrained apparently:

Retraining the window:

1. hold the up button until the window is up and then for ten seconds
2. hold the down button until the window is down and then 10 seconds

unless you changed the motor...
Standardising the new power window motor
1. Switch on ignition.
2. Open door window completely by continuously actuating the power window operating button, and then close window. Press power window button until the window is closed and is switched off by the blockage detection function of the power window motor. Standardisation is then completed.

As far as the stereo not coming on, I will have to pull it out and check the fuse behind the head unit. Hopefully that will fix it. These are the only two symptoms I am seeing in the car after the mishap. No CEL, no other lights, all the diagnostics at start up seem fine. I hope nothing else went wrong with any symptoms that I can't see.

I may attempt trying to remove the alternator and replace the reglator myself thanks to pelican parts and buy whatever parts I need from them.

Thanks for all the replies