Ok, here's the synopsis of my troubleshooting. And I think I'm more confused than before:
1. I disconnected the alt, and the flickering was minimal. I was probably only notice it because I was really looking for it. I notice most in my rack lights, maybe they are vibrating from the idle of the truck?
2. I reconnected the alt, and the flickering seemed to be gone. Then I rev'd the engine, and on release the pulsing picked up again. It stayed during idle, and increased frequency when I gave it more gas. At about 3500 rpm, the pulsing settled down. At this point, I check the output at the battery at it read at 13.8V, which is a little lower than before.
3. I disconnected again, just to check, and the flickering/pulsing again was minimal. I let it run for about 3 minutes, rev'ing the engine a few times with no change.
4. Reconnected, and the pulsing was back, but much less noticeable. Here's where it gets confusing; I rev'd the engine, the flickering almost stopped (to the point where probably no one else would notice it) and it stayed at a very minimal level. I let it run for 7-10 minutes while I put my tools away, and it stayed steady with very minimal pulsing, to the point where I could only see it in my rack lights during idle. As soon as I touched the gas pedal (applying so little pressure that the RPMs didn't even go up) any trace of flickering went away completely. So, it seems that the pulsing has gone away, for now.
I'll be taking it up to the PCRC meet on Saturday, which is about a 2 hour drive. Hopefully, I'll be able to determine if it's gone, or just a temporary quirk.