Tom,
Im not sure if any of this will help you, but I wanted to post some of my config edits that I did to get my x-arcade working with retropie. Keep in mind that I have the newer board in mine with a usb output (instead of the ps2). I went into /opt/retropie/config/all/retroarch.cfg and edited the part about keyboard inputs to this:
input_player1_a = z
input_player1_b = shift
input_player1_y = ctrl
input_player1_x = alt
input_player1_start = num5
input_player1_select = c
input_player1_l = space
input_player1_r = x
input_player1_left = left
input_player1_right = right
input_player1_up = up
input_player1_down = down
and also the next part for player 2 inputs:
input_player2_a = e
input_player2_b = w
input_player2_y = a
input_player2_x = s
input_player2_start = num6
input_player2_select = rightbracket
input_player2_l = q
input_player2_r = leftbracket
input_player2_left = d
input_player2_right = g
input_player2_up = r
input_player2_down = f
Maybe this will help, not sure.