Welcome aboard, VoltaTom.
Since you mention not being sure if pinball will work with your setup, I recommend loading the software before you start making sawdust.
VPForums.org has a step-by-step install guide that will walk you through the whole install process. ("Getting Started" pulldown menu in the upper left.)
Visual Pinball (VP) was originally designed to be played on a keyboard so that makes preliminary testing very easy.

If you want tables that require less processor and video power, try some of the VP8 tables at VPForums.org -- the physics emulation isn't as good as VP9, but it's still lots of fun.
The VP8
Creature from the Black Lagoon table should give your system a pretty good workout.
You may also be able to improve your system performance by shutting off unnecessary processes like virus scan, automatic updates, etc.
VP uses the Graphics Processor Unit (GPU), so adding a video card (even an inexpensive one) can do a lot to improve performance for pinball.
VP is optomized for Nvidia cards -- as A1pharm observed, ATI cards don't work as well.
I'm going for 6 buttons per player + P1 & P2 start + P1 & P2 coin, but also want pinball flippers.
There is some overlap between the pinball flippers and MAME buttons -- you wire them in parallel by either running a wire from each switch to the encoder or by wiring them like this diagram shows. If you put Left MagnaSave and Upper Flipper on one button, wire them like below or you'll get P1B1 and P2B1 both triggering at the same time when playing MAME games.


Also consider using Goldleaf buttons for the flippers -- great feel and lower profile so they're less likely to run into anything else.

I'm not sure what to do about admin buttons (enter, pause, escape, other functions?) - Also planning on having several USB ports on the back
For what you've described, P1/P2 Start, P1/P2 Coin, Pause and Escape should work fine.
Move the Enter to the front for pinball Plunger/Ball Launcher.
Some people like shifted functions, but there is the potential for unintentional functions being triggered.
Any button with a shifted function that is hit while the shift button is pressed will output the shifted function.
Problems like bringing up menu settings or accidently exiting aren't
likely, but they are possible during normal gameplay.
Good choice on the USB ports for adding an analog stick, gamepad, etc.
If PL1 (scott) weighs in, listen to what he says, he's a pinball fiend and will give you great advice.

Hopefully more friend than fiend.

Scott