Aha! Good work tracking it down. Figures it's the alarm, those things are a menace.
Joining the two black/yellow wires will bypass the alarm. I did that on mine, for a while, but later developed an intermittent weak start/no start issue (acted like the battery was dead, then cranked right up the next time I turned the key) that didn't clear up until I removed the alarm harness in its entirety. I'm not sure what was wrong at that point, given the alarm brain was already in the bin, but I haven't had a problem since the harness joined it there. These systems were installed after the fact, so they're pretty easy to make go away. Two or three wires are scotchlock'd into the harness, but most of them plug in between the truck's actual harness. So you unplug the ignition switch from the alarm harness, unplug the alarm harness from the truck harness, plug the ignition switch into the truck harness, and it's like the alarm was never there. Same deal for the door locks, at the A pillar IIRC. Two or three wires go through the firewall to the siren and hood switch, but they're bundled with the wiring for the fog lights, so don't just cut the lot. The alarm harness has each wire silkscreened with its purpose, which the main harness doesn't, so if it doubt, look for the silkscreen.
There's a TSB with the alarm system wiring, I'll see if I can dig that up again.
I'll bet if you plug the door lock timer back in, the power locks will work properly again, now that the alarm isn't feeding it garbage.