Most people will probably find this ridiculous, but since it took a fair amount of research and trial and error I decided to do a quick write-up. I've been using a FM modulator to connect my iPod/iPhone to my stock Craig. I have the type that's a hidden unit and connects in-line with the radio antenna. It was literally a 99 cent eBay find, so expectations were quite low. It worked OK but would always pick up a little interference from neighboring radio stations and whine from the alternator. Since I hate having extraneous cords around I didn't like the tape deck to headphone plug route, either. I also don't want to buy an aftermarket head unit as that would change the aesthetics of the car.
I decided I would hardwire an auxiliary connection directly into the head unit as is common with most new vehicles and do away with the FM modulator. The process was basically to tap into the circuits just before the volume/fader/balance controls and the amplifier so I could make use of the standard audio controls and the boosting capabilities of the amp. I also needed a way to rid of all other sound input (i.e. the radio) so the only sound going to the amp was the auxiliary. Since the radio is always on I spliced a switch into the main radio power circuit. This allows me to turn off the radio receiver functionality when using the aux input and therefore no interference. You could just tune the radio to an unused station and forego the extra switch, but even then you get some background noise and hissing which is undesirable. I fed the cables through the dash to a convenient area where I could keep the iPod and the switch.
The hardest part was digging through poorly scanned wiring schematics to try and find where to tap in and researching obsolete amps and pre-amps. But in the pictures below I've outlined what ultimately needs to be done to perform this, should anyone want to.
Also here are some links to relevant wiring schematics:
This is the bottom of the volume control potentiometer where I tied in the aux Connections. Solder leads onto the 3 points circled. 1 is for right channel +, 2 is for left channel +, and 3 is what I used as a common ground for the two. The purple and white wires are stock, in this photo I haven't added my aux leads yet.