I have a 2004 civic ex sedan neither rear window works (up or down) also includes the switches on the rear doors and the master control any ideas where to look

 

make sure they're not locked out on the master

 

If not locked out on the Master switch at the driver's door as mentioned, then may be related to the wiring issues you were having with the audio to speakers? Otherwise - troubleshoot the switches and regulators and fuses #24 (20A) and #25 (20A) in the under-dash fuse/relay box.