Upon the advice of some people over at BYOAC I changed d3d to ddraw and then changed the following settings:
switchres 1
hwstretch 1
resolution 640x480
The picture is now completely rectangular and fills the screen (XP still looks off and so does MaLa but hopefully I can fix that later... well the MaLa gamelist display at least). With these settings enabled I'm forcing every game I run to display in 640x480 mode which isn't the end of the world. There might be a few games that look messed up running in this resolution but not many and certainly not to the untrained eye.
I also was able to launch Popeye for the first time ever on the cabinet - every previous attempt I was greeted with an "out of range" error message... it is one of the games that looks a little different than I remember it (not as sharp) but I can change "hwstretch" to "0" in a specific popeye.ini file. I'll have to continually tweak the individual .ini settings for the games that don't look quite right but there shouldn't be many of them.