Arrgh, I'm going a little crazy here. The good news is that the new PCB has more or less eliminated all jailbar interference. The bad news is that the clock doesn't seem to be stable! In some circumstances, it'll end up skipping clocks, resulting in weird artifacts and a skewed image. I'm seeing what I can do to stabilize it on my MV-1C, but it's acting strange. I will see if my MV-2F acts the same way.
If I can't solve it for this iteration of hardware, I'm not sure what to do. This project just keeps getting more and more expensive every time I have to iterate on it. I think I'm going to have to sell off some of my extra Neo systems soon...
EDIT: Well, it's perfect on my MV-2F. I have a late generation 4-slot I can try it on too, and I'll be getting my MV-1FZ soon. I'm willing to believe my MV-1C is a bit wonky, as it's the one I Had to repair and deal with the latent vblank interrupt issues on. Really glad to see the MV-2F run it without any issues, I was getting pretty worried.