Just a couple of things for you to think about:
If you like to play Neo Geo games, you might want to reconsider the 7 button layout. This layout allows you to use both the 6 button fighter layout as well as the 4 button Neo Geo layout.
Since you really like GT, it may be worth having the dedicated buttons for it, but it is not mandatory. You can map any of the other buttons for use in the game. Same would apply to the 2 other extra buttons.
In MAME, there isn't much use for mouse buttons, so you could just wire all of the buttons to the ipac. I would expect some odd behavior if you wired buttons to both. On the ipac, you can use the shift function to make any of the buttons dual purpose. If you want to have mouse buttons for configuration, that may make it worth it, but they might be better off up by the other admin buttons or on the sides of the CP. I found that it is usually just easier to have a wireless keyboard and mouse nearby if you need to do any configuring. If you are using an arcade monitor, you will want to use remote desktop for all but the most simple windows stuff.
I always suggest doing a mockup on hardboard before building the panel. It is cheap and easy to work with, but also strong enough to allow you to test out the controls in game.