So, I finally rotated it! A friend was supposed to come over today and help me do it, along with drill some holes in my panel so I can fit my sanwa stick properly, but when he didn't come, I decided to do it myself. After very carefully taking the screws out of the frame and with my other arm as far away as possible; touching the frame to see if it had any electrical charge, I started rotating the monitor.
What I learned was - monitors are about 3x heavier than you expect. I'm a pretty healthy guy, gym three times a week that sort of thing, but GODDAMN that thing is heavy! It took me ages to rotate the monitor.
Wiring wise, one connector came out, and the degauss coil cable was only just attached. I removed the degauss coil cable and rotated the coil so the cable would reach. The yoke connector that came out, I wasn't so sure about. There's two places it can fit in the arcade board. The only documentation I have on the board is the below image, not so useful.

(documentation - click for larger)

(monitor board, yoke connectors straight center - click for larger)
I found the yoke connector only fits one way, so I stuck it on "A", and booted the cabinet. Besides the high pitch noise the monitor makes, it also crackled a lot. The crackling lessened the longer it was on, but it still crackled quite often.
Looking at the screen, the graphics were messed up. The cave logo appeared, upside down and distorted. The game then proceeded to run, with distorted graphics. I powered down the cabinet and after some time moved the yoke connector to the second place it would fit ("B"). The game booted up the same way, I rushed to get the camera, and the moment I came back the screen turned off (though the machine was still on). I promptly turned the cabinet off. Doesn't smell so great in the back of the cabinet.
For now i'm going to leave it, and try again tomorrow. If anyone has any advice, please let me know. I know I need to degauss the screen at some point, but it's definitely not the issue I was having.
I think tomorrow i'll also swap out the ibara board for die hard arcade, just to be safe
