hi all.. 
i am new to this wonderful site.
i am just getting into the whole arcade & mame thing & i just bought the project arcade book with cd in hopes of possibly building a complete mame system.
Welcome to the Lunatic Asylum....

You've just set yourself on the road to total madness.
With Jamma boards the high scores are usually retained by the the battery backup on the board. Does your board have any dip switches... there may be a service switch for resetting the high score table. You may find that you can re-set it by putting the cabinet into service or test mode, using the dip switches and the on screen options.
Best bet if nobody on here knows the exact answer, is to get hold of a service manual for that machine.
If there isn't a dip switch set, then it may be possible to remove the on board battery for a few hours to get it to reset. BUT!! Be very careful!! confirm first that your board does not have a suicide chip! some boards, when they have the battery removed actually lose a small piece of code that will then prevent them from ever running again. This was to prevent people from bootlegging the roms.
Hope that helps....
Best Regards,
Julian (Fozzy The Bear)