That sounds like a pretty cool idea...I have a few items though that I want to mention about this.
The shooter-ball-tube-switch is a neat idea. The only downside I can think of is that the switch would only send a quick keypress, so the plunger in vpinmame would probably only register a light ball hit, so the ball probably would not even get onto the playfield. You would need a way to simulate the switch being held down for a couple of seconds to give full power.
Do you really need actual flippers? Regular pushbuttons would be OK for this...
For the table bump pendulum, you would need three different sets of contacts (one for left, one for right, and one for forward/back). Not a big deal at all...something like this:
_
| o |
Where the o is the pendulum, and the lines are three contacts. This should work out good!
Good luck on this, and make sure you post some pics when you get it working...it sounds cool!