All GI is powered through connectors J120 and J121 on the power driver board. One goes to the backglass, one goes to the playfield. (And I guess J119 goes to the coin door, too.)
If you've got a problem affecting both, that might suggest a problem on the board, like a broken trace somewhere.
You're number one resource for diagnosing the problem is PinWiki. I've become quite familiar with the General Illumination Problems section of that page (not by choice, of course), and they information there and the procedures they recommend are spot on. You've gotta start with the easy stuff first, as well as the things that are most likely to be the cause. Luckily, they've got it all laid out in the order you should do it.