On the Neo-Geo forum there's a guy who's sucsessfully made LED replacements. He created new PCB's and LED panels. Last I heard he was having computer trouble that was delaying progress. The new PCB's function exactly like the EL panels and they actually run of of the same line as the original one, so they're essentially "Plug-and-play". He (last I heard) hasn't started selling them, but they were expected to cost 150-200 dollars, which in some cases is cheaper than EL, but the LED's basically last forever (compared to the EL's). I'll edit in a link when I find it!
*EDIT* Here it is, it's an interesting read. The pictures are on page 5.
http://www.neo-geo.com/forums/showthread.php?t=209601