I'm 10,000 words into this RPG as of today. I'm estimating another 1-2,000 in the Operative's Handbook, and another 5-8,000 in the Operations Manual. The Armory, Equipment, & Motor Pool Guide is going to be something I work on separate to the RPG itself; I'll only be working on it once the two-part Player / GM books are finished.
The Operative's Handbook is rather short - it's only going to contain the bare minimum of information needed to introduce the player to the setting, help them create a suitable character, and lay down the basics of mechanical gameplay and combat, as well as provide statlines for a handful of weapons.
The bulk of the RPG focuses on the Operations Manual, primarily expanding on rules that the players don't need to worry about when starting the game, as well as advice on how to plan and run the missions, statlines for the bad guys, and a listing of reference materials for both players and GMs. If you want a comparison, look at the 1st edition D&D PHB and DMG and compare the sizes of the two; then remove all the spells from the PHB, and compare them again.
Here is the 1 1/2 page table of contents as it now stands. I'm sure it will change and expand as time goes on, but I see there everything I think I need to include, at least in version 1.0 of this RPG. If people can think of something they feel is missing, please let me know. Also, keep in mind that the page counts are deceptive; I've filled out some sections completely, others only partially, while still others just have a header as a placeholder for the ToC.