Top-Left: P1 , P2, Start
Top-Mid: No 4 way, Spinner, Player1Button1, Player1Button2 (these buttons would be shared with the buttons on the P1 controls)
Top-Right: Shift, OPEN, OPEN (advice needed) Should I add buttons for admin functions?
P2 Start should be on the right half of the panel.
As long as you have at least these functions, you should be fine:
P1/P2 Coin
P1/P2 Start
Exit (Escape)
Pause - Not too near the escape so you don't accidently exit the game
Menu (Tab) - Keep as a shifted function if you have kids or friends that fiddle around with settings, use a dedicated button if you like to fiddle with the settings
Other admin buttons may be needed, depending on which other emulators you will be using for NES/SNES/N64.

Pinball: This is another part advice is needed. I had a X arcade so with the 4 buttons on the sides, I mapped the L/R flippers and L/R nudge. After reading posts here the standard seems to be L flipper, L Magnasave, L upper flipper (then the same on the right). So am I correct that I need 3 buttons on each side (and 1 in the front for the launcher). I know a few of these share buttons with the P1 controls.
The first flipper is for the main lower flipper.
The second is wired for both upper flipper and Magnasave. There aren't that many tables that use Magnasave, and none that I know of use both upper flipper
and Magnasave. By wiring both functions to one button, it keeps it simple and allows you to play pretty much every table ever designed with full functionality.

For people using buttons like Ultimarc's Goldleaf that only have two terminals, there is a way to wire this using two diodes so that the flipper can trigger both inputs, but the associated MAME player buttons won't trigger the other when you press it.

For the left and right nudge buttons, you might want to try putting it centered and below the two flipper buttons so they form a point-down triangle or an L-shaped layout.
(Left side view)
2 1
or 2 1
3 3
1. Left Flipper
2. Left Upper Flipper/Left Magnasave
3. Left Nudge
Test the layout on a cardboard box to verify it will work well for you at that height/angle/range to the monitor.
Forward nudge and launcher buttons might be difficult to reach, depending on how much overhang you have on the front of the CP.
Overhang on the sides can also interfere with reaching the flippers, L/R nudge.
Scott