Update: I drove around with everything connected, but I never used the remote to start, only the key. When I hit about 30 miles, the CEL went out, and the transmission had been shifting fine the whole time. When I start with the remote, the truck wont go into 4th (even after I "deactivate" tell remote start by using the brake) and the light comes on again. So basically, I only have a problem when I use the remote to start the truck. ?___?

On GM trucks you must power up the transmission circuit with the remote starter or you get your exact problem.

Good to know! Best advice yet. How exactly do I do that?

Another update: When I start the truck with the key, all is fine. When I use the remote to start, my solenoids are not getting enough power. This morning, I was looking at my fuses, and the one that feeds the relay for ignition 3 was blown (20 amps). I have attached a picture of the manual for the starter, I followed it to a tee. What would be causing ignition 3 to draw that much more than ignition 2? Does ignition 3 feed the trans power?

another, 'nother update: I called customer service at directed electronics, and they told me simply to replace my 20A fuses with 30A ones. I did that, and the same fuse blew that blew before. I'm pretty sure the white wire feeds the trans, so why is the white/pink wire drawing too many amps? And why don't I get codes when i start with the key? I am stumped. The only thing i can think of is that the 2 relays I bought aren't 30A, is there a way to test them?

anyone?

Don't ever replace a fuse with one of a larger value. I don't care who told you that. Advice like that is irresponsible at best.

The infamous transmission wire is a white wire in the ignition harness. It needs to be powered up by the remote start during activation. This wire needs to see 12 volts during crank and run. In other words, it is a "true" ignition circuit. This should be the pink/white from the remote start. If this wire is not powered, the check engine light will set and the transmission will not operate properly (not shift out of second, or not downshift sometimes). This will almost always cause severe transmission damage in a short amount of time if not resolved. This should not be extremely high current (it's about a 14 gauge wire); any Bosch-style automotive relay is rated at 30A, which would be plenty for this circuit.

To sum up Chevy wire colors:
Batt +12V: Red
Ign 1: Pink
Ign 2: White
Ign 3: Pink/white (this wire is not on all models)
Starter: Yellow or sometimes purple
Accessory 1: Orange
Accessory 2: Brown (sometimes not used)

Test the white ign 2 wire to make sure you have the right one. It will show 12 volts in run AND crank position. It can be found along side the other wires (in the same harness).

If this doesn't take care of the problem, you may already have other issues with the tranny at this point.

Great advice! I will check that and get back. Since disconnecting the remote start, the transmission has been shifting smoothly as usual (smoother than some other 160k I've driven)