1.)all of my daisy chained wiring from the "common" terminal of the switch wire to the ground terminal on the ipac correct?
Correct!
2.)I have 4 dedicated buttons to wire (exit, pause, etc.) in the current mame configuration they are a shift function. To make them seperate functions all to themselves, I reprogram my ipac (move the jumpers, etc.) So can I just pick any unused inputs on the ipac to wire them to and specify them in my program?
Pick any unused inputs on the I-PAC and wire them in. For MAME, you have the choice of re-programming the I-PAC or re-programming MAME.
For example, let's say you are not using P1B7, which is I think "C" in the default I-PAC program. You can either connect your Pause button to this and Re-program the I-PAC so this input send P . . . or leave the I-PAC alone and in MAME change Input (All Games) so Pause uses the "C" key. Either way.
3.)I have two mouse trackball buttons. Where are they wired to. Maybe the same inputs as my 4 way dedicated shoot and jump buttons? Which would also be the same input as two of my buttons for my 8 way player 1 control. that seems like a lot of wires to one or two inputs. And would this allow these buttons to double as right and left click this way?
Option 1 is fine for MAME, but if you want them to right and left click in windows, you need to wire them to whatever the trackball interface is using for buttons. What interface do you have for the t-ball (hacked mouse, opti-pac, ME4, Happ, etc?)
4,)Lastly, whhat in puts are best wire my two side pinball buttons to?
The pinball games in MAME are probably using L Ctrl and L Alt, but I'd want to verify that. If you're gonna be using Visual Pinball, I think you can assign the buttons to anything anyway, so it really doesn't matter I-PAC wise. If you are using any Pinball emu's that don't allow you to remap inputs, then wire the buttons to the corresponding I-PAC inputs, unless there isn't one, in which case, you'll be re-programming the I-PAC, so again, it doesn't matter.