"The main elevator (seen in the Bete Noire layout), is the key to many guesses of room locations.
It has 5 buttons in it (presumably B2, B1, Main, 2, 3), although we cannot see the buttons clearly enough:

B2 is Autopsy - as would be expected.
B1 is Abby's Lab; a half floor down, based on the high windows in her lab, at ground level.
M is rarely seen, but visitors are sometimes dropped off there so we know it exists
2 is the Bullpen
3 is MTAC, and presumably the Director's Office

I have presumptions:
-Garage is at the back of Abby's Lab somewhere. Since people walk by Abby's window, she's at the front; the garage makes sense to be at the back. As well, vehicles would go down one half-floor this way; rather than 1.5 floors if the garage were behind autopsy.
-the Armory, first seen early in Season 10 (Ep 1 or 2?) - I cannot place it; but B1 or B2 would make sense, for security reasons.
-the break room is likely on the 2nd floor with theBullpen - and Interrogation is believed to be under MTAC.

But there are inconsistencies in the layout referenced through the show.
-for example; more than once, Gibbs is in Abby's Lab when he has to 'go UP to Autopsy'.
-the Bete Noire layout, shows that the below-ground level building is extended, and its primary space is turned 90degrees from the direction of the upper building.
This is unlikely for architectural design, and physical stability, issues.

I have just started creating a 3D model of the building; I will use the Bete Noire layout to put the floors together; then work at it from there.

"