1) To install the track ball without a mounting plate, would I use a 2.25" inch hole saw for the trackball and then drill out the other 4 bolt holes? I am mounting this on metal and a plexi layer. Is this way too thick? The metal is thin and so is the plexi.
The lip of my 2 1/4" wico TB is only 1/16" of an inch high, which is usually the thickness the the metal plate of CPs. However thick the plexi is will be how much the TB is lower than it should be, IMO. (Assuming you have a 1/16" think metal CP.) 1/16" plexi isn't that bad, 1/8" is way too think for this IMO.
If you can stand it, though, yes just drill a 2.25" hole. If the metal is 1/16" think, however, you can drill the plexi hole as small as 2" (if perfectly centered with the metal hole, and you'd want to bevel the plexi edge too). Make sure the bolt holes form a diamond with the points above, below, left and right of the ball hole (not a square with the edges parallel with the top and sides of the CP).
Ignore first paragraph if the new wico TBs have "golden tee" high lips (3/16").
2) Is there any molex connectors I can buy at radio shack to fit the 4 pin connectors on both ends of the trackball?
Yes, in the better radio shacks. The smaller ones probably won't have it; I think only two out of four radio shacks around home or work have them, but I wasn't looking for the part you are. Bring the TB so you can see if they fit, just in case.