What is happening in test mode? Are you getting any errors or beep codes?
First thing to do is check your ROMs, particularly the VROM (the single one at the top of the board). I've also seen marginal vector RAM cause glitches. Normally these things are flagged in test mode, but I've also seen cases where the bad RAM is marginal, so it passes self-test, but causes in-game issues. I've seen some cases like this however where if you leave the board running for a few hours, and let it warm up, eventually you'll hear it start reporting beep codes, when the chip fails bad enough to cause a reset, and trip the self-test. These cases are rare, but I've seen them more than once, so I figure I'd mention it.
If it's purely a graphical glitch (and not affecting gameplay, causing resets, etc), and it's not a marginal ROM or RAM, then it's likely something fairly late in the digital chain. It's hard to pin it down to a single chip, but you should focus on the Vector Timer and X and Y Position Counter sections of the schematics.
You can focus on the counter chips in those sections. One trick I use is to check all of the inputs and outputs to make sure they're toggling, but also check the carry signals (that go between counter chips), as I've seen cases where the inputs and outputs will be toggling, but for whatever reason one of the carry signals isn't, which shouldn't normally happen.
Looking at your video again, it almost looks like it could alternately be something in the Z blanking section. This is on the last page of the schematics, and comes together in the LS164 at K9 (or K10, depending on which PCB rev you have). However the BVLD and BLANK signals that come into that chip come from the position counter section, and the State Machine, respectively. One additional thing you can check is the PROM at C8 (or C9). If you haven't cleaned that socket, do so. (It's often socketed, but isn't on some boards). If you have a working AD board, AD uses the same PROM, so you can try swapping them, and seeing if that fixes it. You might want to try this first actually, if they're both socketed.