Since it worked before I disassembled it and doesn't now, a wire or connector must not be seated well. Long story short, I managed to get it powered by removing some connectors, so I'm in the process of trying to figure out what's going on.
From what I can tell, I figured out the problem. I removed the front panel and noticed a small ribbon cable dangling. It must have somehow came out due to not seating it well. After re-seating it and haphazardly reassembling it for testing purposes, the unit powers normal.
The odd thing: at a random point when it wasn't working, it somehow began working normal (minus the power button wasn't doing anything). Immediately upon plugging in AC, the scope would boot. Eventually it stopped working again, so that threw me for a loop because I was looking for a looks connector on the Acquisition Board since I had removed it.
Since I finally got it to boot, I decided to let it go all the way to test the encoder. I turned it several times CW and CCW, and the waveform span and shrunk as expected. It physically fits well, the shaft is a mm or two shorter (hardly noticeable) but won't affect supporting a 3D printed knob, and possible a larger diameter shaft which isn't an issue since I'm 3D printing a knob.
Now I need to reassemble and tinker with a 3D print for the knob someone was kind enough to create for me.
The only other upgrades is adding another 256MB RAM, a SSD, and duplicate my other SSD that has XP on it (I have a backup SSD for my other scope, so I'll use that in a duplicator).
As always, I appreciate all the help, in this case, with the encoder. This will (hopefully) be my second fully working Agilent 54831M (which will be upgraded to the other 1GHz BW model once I remove a resistor) thanks to the help of everyone on here.