Thanks Calamity, I tried a PCB and the vertical lines were still there. So I decided to try another MS9-29 chassis and the problem went away. So the problem wasn't being caused by the J-pac or wiring, it was actually an issue with the chassis.
The chassis I put in is auto switching between 15Khz and 24Khz. As it's auto switching I thought I would try the MS9-29 Monitor Preset in VMmaker rather than the "GENERIC"
// NANAO MS9-29 (retrorepair)
monitor_specs0 15450.00-16050.00, 55-65, 3.91, 4.70, 6.85, 0.190, 0.191, 1.018, 0, 0, 288, 448
monitor_specs1 23900.00-24900.00, 55-65, 2.91, 3.00, 4.44, 0.451, 0.164, 1.048, 0, 0, 480, 768
I also set the mame.ini to "ms929"
Unfortunately 15Khz isn't centred correctly and I tried Narc (24Khz) and the screen went mad, so I quickly exited the game.
Are you sure the MS9 settings are correct as everything works perfectly and centred correctly when set to "GENERIC" and "arcade_15"