Hi there
I am running a the same sort of system you want.
I have the dos version of mame because it is so much easier to hide windows, much faster to boot (around 5 seconds) and I only had to know how to change directories to make it work

If I need to do anything else to the system I just open a dos window from my front end and run windows 98.
I was thinking of a Keyboard hack but went with the "ultimarc" I-PAC because of the ease of use and the PS2 thro port enables me to conect up a keyboard to make changes ect.
If you want to know any more about my MAME system just ask

Coldrain