If the 9000 accepts output at its native resolution from the PC, I would connect it directly to the PC and forget about the J-PAC for the purposes of video. Use the J-PAC for everything else (ok; not audio. JAMMA audio is monoaural.)
People continually poo-poo LCDs on this forum, and that is a bit of a shame; with a tiny bit of effort, they can look really good. Given that CRTs aren't manufactured anymore, eventually most folks will come around to the practicality of LCDs. There are even a few 120hz LCDs today that use backlighting tricks to virtually eliminate blur. Technically, the blur is still there, but the backlight is off between frames, so you don't see it.
Drive the LCD at its native resolution, if you can. Then tweak HLSL to look good on that monitor.