Thanks! I actually wound up adding them to <baseInputCoes> in LEDBlinkyControls.xml and that seemed to do the trick, except that the button numbering seems to be off by one. On the GPWiz, button 1 is identified in mame as Joy 3 Button 0, and LED Blinky calls it JOYCODE3_BUTTON1. Same for all of the other buttons I have connected in the 1-16 range (buttons 1,2,3,10,11,12, and 13 are the only ones I have connected from 1-16) However for button 21, mame identifies it as Joy 3 Button 20 and LEDBlinky also calls it JOYCODE3_BUTTON20 (instead of BUTTON21). Same for all of the other buttons above 16. Not a big deal for me since I am not using all of the inputs, but based on this pattern it seems Joy 3 button 15 and joy 3 button 16 in mame might both be identified as JOYCODE3_BUTTON16 in LEDBlinky.
On an unrelated note, right now I am using the trial version. I know that the splash screen will go away when I purchase the license. Is anything else affected? Specifically, it takes much longer to launch a game from mala with the ledblinky plugin. Will that speed up with the license?