Well I ended up pulling out the head unit once again, this time to install the e-brake bypass thingie and an AUX jack. Before buttoning everything up, I connected and fired up the Pioneer to see if the bypass worked, and it did/does. Plays DVD's and everything now.
After that, I decided on a good spot to install the AUX jack, drilled a hole and mounted it. Then came the part of finally running the "Auto TA/EQ" function. For some odd reason, it had the output level of the door speakers way down at -16 and -17. All I could hear was the dash speakers. It also threw the crossover way up at 8 kHz and jacked the treble way up. Horrible!
Then again, it might have something to do with the old TOTL Onkyo receiver calibration mic I'm currently using. My main concern is proper time alignment than anything else. I can do levels and EQ myself.
Anyway...