The first and biggest concern I have is cutting through the MDF.
If you don't want to buy a jig saw or router, there are the roto-zip and dremel. A little checker are drill bits for normal drills that can be used to cut. 3/4" might be a little on the thick side for them, since they aren't as good as the roto-zip or dremels that are made to do this. You could also drill holes in a line with normal bits, but that's not that easy either.
Note that you can cover the hole for the TB case, which would mean the edges don't need to be clean. The mounting plate is the easiest surest way to do this.
Second, should I get an Optipac or a trackball with a built in USB/PS2 encoder? I'm going to eventually add a spinner
I'd go optipac in your case. I little more in price, but easier on the wiring and connecting to the PC. If you run windows & windows mame, I suggest the USB version.
Third, what kind of trackball should I get? My budget is around $150, including everything necessary to mount and interface the trackball. This will cover a Happ 3", Optipac, and mounting plate. But is that the best trackball I can get? Also, are there any differences aside from asthetics between the different colors, translucent balls, and solid balls?
Between my happs, betson, and wico 3" TBs, I like the happs high ligh (aka golden tee) TB the best, but would be happy with any of them. Order of likes:
1) Happs highlip: longest spin, loudest sound, smallest case (for a smaller cut out hole).
2) Betson: second longest spin, biggest case
3) Wico: shortest spin, same size as betson case except the cut corners are cut more.
4) Happs highball: same as highlip, except the ball is too high for my style of play. I knock the ball off the rollers too much, and the ball is too verticle were I hit it my hand gets hurt. Inside of case scratched my black ball pretty badly before I sanded it (the case); probably caused by my knocking the ball off the rollers so much, or maybe that I bought the highball parts individually instead of as a complete TB.
Solid color balls are heavier than the translucent. I think the perfectly clear one is even lighter than the translucent. The different weights will change the spin time (heavier=longer), ease of start/stop/change direction (lighter=easier), and maybe how well it "sits" on the rollers (lighter=easier to come off or slide on roller?).
Clear stratches the easiest. Not sure about ease of scratching of the translucent, but I think scratches would show more on the trans than the solids. (All I have are solids)
As far as your other questions go, other people can answer far better than I can.
They look good to me.

Urebelscum should write a FAQ or something, he always answers these questions 
I have been meaning to do a full review since forever, but never have gotten past the primary testing of the first TB.
While we're here, has the community decided on a 'consensus' best way to mount the Betson High Lip? I'd like to have no visible plate or bolts, if possible. I also have the 1/16 Lexan on top.
High Lip & 1/16" lexan, I think (but never tried) I'd get happs mounting kit, zinc (the one with posts stuck on the bottom so no bolt on top), and 1.5 mm (or 2 mm or 1/16") laminate (include any designs on it, or fake mood grain if you want that look for the whole top of the CP). I'd route 1/16" of the wood for the plate to be level with the rest of the CP. Cut square hole for the TB case to fit on the plate. Place plate on wood, laminate over wood and plate. Carfully drill 3" hole in laminate, using in place plate hole as guide. Lexan over laminate, and again, carefully drilling 3" hole in lexan using plate and laminate hole as guide.
Problems: can't remove plate without removing laminate, costly.
Pluses: plate covered, no bolts, lip basically even with top of lexan (within 0.5 mm)
I'm planning on doing the above, except no lexan. I'll need to shim between the plate and the TB to drop the lip the ~1.5mm (~1/16") it would be above the laminate without the shim (durring testing, nylon washers seem to work fine).