Congratulations on the new cabinet.
Given the position of the current buttons, I think that making a new panel is in order. You might be able to get away with drilling new holes more appropriately aligned for NeoGeo and patching the old holes, but I'm not sure you would be happy with the result.
My impression here is that you want this to be a NeoGeo cabinet, right ?
The good news is that the Neo Geo 1-slots are all JAMMA.
The bad news is that your JAMMA harness quite possibly does not have button 4 wired (since true JAMMA is 3 buttons). You will likely have to stuff the wiring for button 4 into the appropriate slots on the harness (25 and c). This is not a big deal, although it may sound like it.
The first thing you should do is go to HardMVS and download the manual for the NeoGeo Motherboard you have.
http://www.hardmvs.comThen I would have a look at the edge connector on your JAMMA harness and look at pins 25 and c (the pinout diagrams in the manual will show you where these are). If there are currently no metal pins inside those slots or if the ends of the pins are exposed (e.g. you can solder to them), then this shouldn't be a big deal at all.
If all of this is confusing, take a picture of the connector (on the "wired side") and post it so we can have a look.
Hope this helps.
Cheers.