First off, let me say that I like your boss and counterbore idea to keep the top two pieces aligned but your machinist is going to want to know the tolerances. For instance, make your counterbore .6875 +.005/-0 and make your boss on the opposing piece .6865 +0/-.005 You are going to need this anywhere that you want to maintain a fit. Notice, that I gave the counterbore a nominal that's closest to 11/16, this is because it's harder to measure than an O.D and they can use an 11/16 pin to help measure it.
The only other thing is that Dan's idea will be self-centering and yours will be subject to the tolerance you give it, you could always change it a bit if it matters, to incorporate both ideas.
As far as the O.D. of the pieces that have an O-Ring groove in them, I'm doing a "slip fit" to the ID of the tube. Basically that is about a .001 clearance. This will give the stability. As I sad before, I'm going to adjust the diameter of the O-Ring groove to make it fit the way I want.
My suggestion is to bring the lexan with you and when the machinist gets to the oring groove have him start out a little big on diameter and put the oring on it while it's still in the lathe and try to slide the lexan over it. Wash, rinse, repeat until you've got what you want. That's what I'm going to do and it will only take an extra five minutes.