"I'm not sure what you mean by angle the top. Right now the body is just shy of 2" thick so I have plenty of material for carving. I will probably do the traditional PRS carve but I'll probably get an inexpensive piece of scrap wood to practice on first!"
PRS has angled tops, plus the neck angle. If you don't know what he meant, then do some research. and try to find a original prs to see what that is.
"I agree that it would look odd to have the grain run perpendicular. I do have the option that I could bookmatch the piece of stock and then I can get the grain to run parallel with the body. That piece of stock is 2" thick as well so there is plenty of wood to work with."
+1 on using the grain paralel with the body and neck and maybe all other wooden parts on the guitar.
"But if I do go with a veneer I want it glued on before I cut the headstock out. I think it would be a huge pain to cut it exactly and glue it properly."
Cut the headstock first, then glue the veneer and trim the overhang with a chisel or a knife. that's quite an easy task. you just have to read the wood and know what direction to go with the blade. You can also make your own veneer out of mahogany, I see that you're gonna have LOTS of wood left from that neck blank. IMHO you're wasting way too much wood.
And one last thing, I wouldn't make the neck using the templates. now that you've already glued the ears to the headstock part, there's no way to use that template. but there are many many ways to build a neck without templates.
My way is to taper the FB, cut the fret slots, make the scarf joint, glue the FB, cut the excess wood on the neck, use the safe-t planer to thickness the neck (I place a small piece of wood in the first fret to make the taper on the thickness of the neck) plane the headstock back, use the router to shape the headstock, glue the headstock overlay, trim the excess with a sharp chisel and knife, and then use the router with a pattern cutting bit to follow the FB and cut the neck flush with the fb.
I sometimes do these things in another order. but it has worked very well for me.