dodge truck problem

you mean like a turn-on thump and then no music?

First of all I'd recommend using an external line out converter as these usually performa better than the ones built in to amps.   Even if it didn't make a difference before you should still use it when possible.

Have you tried hooking up a test input to the amp to see if the problem still happens?  And what about using a test amp with the factory speaker wires?

If you can do those two tests you can eliminate a bunch of stuff as possible causes.  The reason I suggest this is because you said you get bass, so that can't mean you've tapped in to a high-frequency-only speaker wire.  Although if that were the case the solution would be to tap in to the wires going to the 6x9s in the doors as they are sure to get the most bass out of all the speakers in the system.

Of course I'll say the same old BS---check your ground, power, and signal connections, and check the sub wires for polarity and proper connection,bla bla bla...

First thing I'd do is get a walkman or a test head unit and hook it up to the amp, and then see what the bass sounds like.

Okie I got another idea.  Instead of tapping in to the wires at the back speakers, or at any of the speakers for that matter, just tap in to the wires in the radio's harness.  You might need an LOC or similar device to match up the signal level as I don't remember if it's a high or low level signal coming from the head unit. 

The factory wiring goes as follows:

rear left positive: BROWN / yellow

rear left negative:Dark Blue/red

rear right positive: Dark Blue/white

rear right negative: Light Blue/orange