Not sure how long ago you upgraded radio but you may need it all to catch up the the truck systems. Turn the truck in, run for a a while like around town, turn off and repeat a couple times. Could also try taking power off battery and leave off for a while, then reconnect and repeat a few on/off cycles.
Assume the feed in and out for the amp is there, but don't know the wiring.
For rear sliding window find one in a junk yard. You will probably need some type of wiring to complete the connection plus the switch. You can get the factory switch from Benny at All Mopar Parts in vendor section. Wiring may be able to get custom work from M²Mods in vendor section, PM him and ask about your plan. He also may have a suggestion for the radio system but realize he is doing this on his personal time and he can help with other wiring needs so support him along with our other vendors whenever possible. Good luck.
