I've never put a finish on a guitar before outside of Tung oil. The wood just popped, that was easily one of my favorite processes in this entire process. It already looks amazing. Now to not screw it up.

Speaking of Tung oil....I want a matte tung oil finish on the neck. Should I pore fill the neck as well or not? Any issue with Zpoxy and Tung oil adhesion? Or is it ok by itself? Doesn't seem like it would work since Tung oil is a penetrator and the zpoxy is essentially blocking the way to the wood.

If you sanded the neck back to bare wood it would work, but leave a couple of spots with z-poxy and the finish will look blotchy. I use Danish oil on my necks with wipe on poly over that. It looks great and feels good too. A matte wipe on poly finish could be the ticket for you. Anyway, I pore fill my bodies with z-poxy but the necks with TimberMate for the reasons above. The TimberMate doesnt block the oil from getting into the wood so it still pops the wood figure very nicely, and the poly looks great over that.
Here is a pic of the back of a headstock I finished with the Danish oil/ Wipe on Poly schedule:


It comes out pretty nice.

Just so we're clear:

There are three products made by Zap that have been mentioned:
- Z-Poxy 5 minute epoxy (PT-36, PT-37, PT-38)
- Z-Poxy 30 minute epoxy (PT-39)
- Z-Poxy Finishing Resin (PT-40)

I don't use the 5 minute (or any 5 minute) epoxy because I have other glues for short working time. The 30 minute is a perfectly adequate, easily sanded and worked structural epoxy designed for gluing things together. I've used it on fingerboard to neck joints and laminations before without trouble, although I currently use WEST systems stuff instead.

Finishing resin (a different product entirely) is what I and others use as a pore filler. It's thinner, easier to apply, easier to sand and possible a little clearer than the 30 minute variety. I allow at least 24 hours to cure before re-coating.

Does this 30 minute version have the same color as the finishing resin? (PT-40, system 3)

I purchased the Timbermate from Stew Mac or LMII. I forget which one carries it. however, if you are pore filling mahogany, and the pores are not too big, you could use a wood putty from Lowes or Home Depot. Just watch out for shrinkage, and I'm not talking about the George Costanza kind!
There was a thread the the UMGF about grain fillers and someone, a prominent luthier if I recall, mentioned using wood putty. I could be wrong, but for small pored woods, it should be just fine.
Min Wax Wipe on Poly is available at Lowe's for sure because that's where I get it. It comes in gloss, semi gloss, and satin if memory serves. Easy as pie to put on. I use good, name brand paper towels as they release little to no lint. Wipe on the thinnest of coats and let dry. Since it takes a while to flash, the surface stays tacky for a while and can attract dust and flying insects. You can knock those off with 600 or 1000 grit paper before your next coat, but I usually do 3-4 coats, knock off the nibs, then repeat until I have the desired build. It builds slowly so don't be in a rush and try to put on a thick coat. You will get a better, smoother finish with less sanding if you do many thin coats versus trying to apply it thicker. I can usually do 2-3 coats in an evening if I put it on thin enough and it's warm enough out.
I use nitro on the body, so having enough time to apply plenty of coats of the poly is no issue. I start when I am starting the box, then keep applying while it dries so I end up with two weeks worth of time to apply many coats of the poly.
One word of caution: Wipe on Poly will not cure over oily woods. The neck in the pic I posted had a macassar ebony back strap and the poly would not cure over it. After about a dozen coats, I had to sand it off, apply shellac as a barrier, and then start over. It turned out fine as you can see, but half of the grain lines were matte finish, half were glossy, and all of them were tacky while the rest of the neck was fine. I have used it on ziricote, bloodwood, walnut, maple and mahogany without incident. That darn macassar ebony was the only problem wood so far. I suspect cocobolo would be problematic as well.
Oh, and I have been using nitro on the front of the headplate lately, but I did do one guitar with poly on there and it turned out fine. Here is a pic of that:

Not a great pic because you can't see the shine very well, but it was shiny. Really. I used nitro so I could bury my logo decal under it and sand it flat.
Good luck and post pics.