I hung out on the forums for a very long time soaking up information before starting, so there aren't really any newb mistakes.
During that time I used an x-arcade tankstick which allowed me to experiment with ergonomics, monitor placement, etc. I even swapped various joysticks into it over the years.
Biggest single regret:
I have a rotating LCD monitor, but the viewing angle from the bottom is horrible. So on 2 player vertical games, player 2's view is darker than player 1's. It doesn't make the game unplayable, but it is noticeable. I wasn't planning on doing a rotating monitor when I originally bought it. Not sure I would have thought about the viewing angle anyway. Since the VESA mounts are off center, I can't just swap in another monitor. I'd have to make a new bracket for the rotating assembly. The current monitor almost touches the side and top when it rotates, so clearance might also be an issue. Honestly, 98% of the time I'm playing the cab by myself so it doesn't really bother me that much.
I'll show other things that I could have done better whenever I get around to a reveal video.
Biggest thing I got right (for me anyway):
Used a powerful enough computer to run Demul, Taito Type X, & modern PC games. I play these other things as much or more than MAME.