I made a small utility that pretty much does the same thing as what MrSalty made, but this should be a little easier to maintain.
You can get it
here.
It's my first-ever C++ project so go easy on me

All it really does is take a map file (included in the .zip with info on controls.xml .88 and mame .92) and translates the input to a number compatible with gpwiz49.exe, then passes it to the gpwiz.exe specified in the (included) .ini file.
The map file is pretty simple:
<romname>=<control>
<control> is the short "constant" from the controls.dat project, with the addition of 'djoy4way' and 'joy49way'.
The newest
ListGen.NET can generate this map file for you, or you can simply modify the default. As soon as I can figure out how to add the expat libraries to my IDE I'll make this a built-in function so you can create the map file with just this .exe.
*shrug* let me know if you have any problems...
-sab