Hey everyone! Sorry about the seemingly late replies on my part, since I'm a new forum user the mods have to accept all my posts manually.
Good news- got it fixed! But, still not sure exactly what was causing it. Here's what I did.
Under the guidance of Ultimaker US Support (thanks Spencer!) I got some help. Turns out I wasn't under warranty anyways, haha. I took a look at the white main board. Nothing looked amiss. All the cables were seated properly, all the locking clips were engaged. No physical damage on the board or anything.
Before the next test, Support did have me unplug the power brick from the machine and the wall, and see how long the LED stayed on. It remained on for well over a full minute.
I had the idea of plugging the X/Y motors into the Z port, and running "Lower Bed" to see if the motors themselves worked properly when plugged into the Z port. The plugs were tough to un-plug, they were definitely seated properly to begin with. When in the Z port, both X and Y stepper motors were driven like normal. So I thought it could be the X and Y drivers.
Then, I plugged the Z motor into the X then Y port, and used "Home Head" to see if the Z motor would be driven smoothly. It was! So, it wasn't the motors themselves, nor was it the drivers.
I went ahead and plugged all the motors back into the correct ports, and... it worked? No jitters, no stutters, everything moving smooth. A bit confused here, nothing fundamentally changed, but the problem disappeared as quick as it appeared in the first place. I'll keep an eye on the machine during the next few test prints.
So technically, all the steps I did from problem to solution were: Factory Reset >> Power Supply LED Test >> Unplug all motors >> Drive X motor with Z port>> Drive Y motor with Z port >> Drive Z motor with X port >> Drive Z motor with Y port >> Return all motors to correct ports >> Motors now move smoothly. Tested using Home Head and Manual Bed Leveling
Thanks for all the help guys, this community has excellent support.