I tried to represents all the main lines of the Pirc Defense to play at a 2000 ELO level. Am I right with the following tree? What I mean by right is I wonder if I do not miss any popular line or choose a bad move at some level.
If you are aiming to use this tree for practical use at 2000 level, you should start in the Pirc tabiya position after 1.e4 d6 2.d4 Nf6 3.Nc3 g6. That's where it all starts, with main choices being 4.f4, 4.Be2, 4.Be3, 4.Nf3, 4.f3. (edit: Also 4.Bg5, 4.Bc4 and even 4.Bf4 as pointed in comments.)
That way, you will not be confused by games without ...g6 at all, like the Philidor 3...e5 or some moderns with 3...c6, 4...Qa5.
I don't think the 1.e4 d6 2.d4 e6?! branch will ever be useful to you. With Black, you won't ever want to play this. With White, if you face it you can tackle it by folowing general rules, and in any case a tree is not useful there. Also, I wonder how this very obscure sideline appeared in your tree. If you use popularity to select lines, have you consider how far 2...e6 lies behind 2...Nf6 ? Have you restricted your base to tournament play, if possible above a certain level (say, 1800) ?
If need be, you can build a separate tree for early deviations, like 2.Nf3, 2.Nc3 or 2.f4 - keeping in mind that they will often transpose later in your main tree in case of d2-d4. But if you have practical purposes, you want to get rid of parasitic information. That will also allow you to go deeper that move 5 - which is mandatory at 2000 level !
After ...g6, playing Be2 and h4 with white is a popular option which is missing in your tree