I recommend reading Edwin C. Fishel's The Secret War for the Union. Fishel makes a strong case that Pinkerton's methodology wasn't in fact all that terrible at first, but that there was pressure (specifically from McClellan) that "the numbers be made large," with a significant factor being the assumption of manpower represented by each identified regiment. (It's fairly dam ning of McClellan...)
Secret War for the Union, unfortunately, only covers things in the first half of the war, roughly up through Hooker's tenure, and only in the East... it really should be called "Military Intelligence of the Army of the Potomac 1861-1863" but that's too dreary a title for the publisher, I guess. But knowing a little about your background, I think you'll enjoy it-- it's about real intel work, not all the usual frou-frou Belle-Boyd-and-Rose-O'Neal-Greenhow trivia.