Raptomex: I attempted this for Win 7 64. The config file was located in AppData. The custom changes I made never took.
I have W7/64 and it worked just fine for me, but I appended the commands to the unnamedsoldier.cfg file, which can be found in the [your mohaa installation folder\]main\configs folder (mainta\configs and maintt\configs for Spearhead and Breakthrough respectively).
I did just use:
r_customwidth "1600"
r_customheight "1200"
r_mode "-1"
Not sure about the FOV setting, as I did not change it, but I assume it works the same way.
vid_restart wouldn't be necessary as this is executed on launch and not during runtime.
Make sure you do not change options in-game after doing this (set everything as desired beforehand), as that overwrites these files. You could make them read-only if you want.