From the shop manual:
System Operation
The 10R80 transmission is a 10-speed, step ratio rear wheel drive transmission that is controlled by a PCM for gas engine applications or a TCM for diesel engine applications. The 10R80 has ten forward speeds, one reverse speed, four planetary gear sets...
If you push the + button, you will see a gear selection number highlighted on the dash. Using S mode, push the + button and look to see what gears the transmission is shifting into. Don't press the - button for this test. This will tell you what gears are being used.
Did you remove #4 spark plug coil (closest to the firewall)? If so, make sure that the coil pack is correctly snapped onto the spark plug. Since there is piping in the way of that coil pack, it is difficult to get the coil onto the plug properly, causing a misfire.
If the alternator isn't charging, check the 125 amp fuse bolted to the battery positive terminal buss work. It might be blown. That is the fuse to the alternator.