...A couple questions and suggestions after following all this...Just trying to help...
...Your lights shouldn't be dimming even if you have a draw from the window switches. This means your alt may test out that it does charge but it is not working under a load as it should or you have a short or loose connections.
...First, pull the battery and alternator and go to another shop other than Autozone and have them bench tested...As I had mentioned before, AZ alt's have been showing up here for a while driving owners nuts trying to diagnose similar problems and they just knew it couldn't be the newer alternator...The battery may also have issues on it's own or due to, previous or current failing alternator..
..If above test out perfect, this is a little more in depth..
...Does the vehicle have an alarm/custom stereo or did it have?
...If no alarm/stereo was/is related, my first thoughts would be the alt/battery, then the new cables and connections (they could be assembled bad too, don't ask as I recently fell victim

), alternator wiring (common with Ford for years), or possibly a short at the master switches on the driver side due to getting bumped or wet...
..I actually helped out a guy who had similar problems and never even new the previous owner had an alarm installed...It was tied into the windows and door locks and he accidentally kicked the wires to the manual on/off for the alarm which created a short..