Sounds like a bad board to me. I'm not super familiar with that model, but all of the Mutoh/Mimaki/Rolands are similar enough they display similar issues and fixes.
Anything crazy happen like power outage, breaker trip, bad storm? I've fried head board fuses just by touching a printer and having static built up.
Dumb question, but have you powered printer down, unplug, let it sit for 5 mins and rebooted? As silly as it sounds, I've had that work with similar issues.
You could look at and smell the boards to see/smell if there is anything noticeably blown. Many times it's not noticeable, but sometimes it's blatant. I worked on one brand of printer and every time the transformer on the main board blew it stunk pretty bad.