You need to alter the repeate rate in the keyboard settings. It's different for each version of windows and buried pretty deep. BUT.... keep in mind that neither mame, nor any other game for that matter, worries about repeating keys. Games use directinput, or something similar that ignores repeat rates. Just because it repeates in notepad, doesn't mean it will in your game.
You've told us nothing about the keybaord interface you are using to hook up your controls, so the rest of the questions can't be answered.
I will reccommend AGAINST hacking a keyboard though. Back in the day it was the thing to do because encoders were non-existant and/or expensive, joystick support was non-standardized and keyboards were built like a tank (in other words a REAL circuit board in the keyboard.) Now days this simply isn't the case. Just buy a keyboard encoder for 20 bucks or so and save yourself a headache.
Also I'm not sure why you are hung-up on re-assigning keystrokes. Mame and virtually every emulator/game out there allows you to remap keys... there's no reason to do it on the hardware end. But if you do wish to do it on the hardware end, most of your keybaord encoders support this anyway.