Definitely pick up SFA. You will want psionics and mysticism. And don't disregard the setting. There are lots of cool ideas in there on how to set up an Agency, and a Threat.
Spycraft handles everything spy-related you can think of. Gadgets, martial arts, tradecraft, etc. The SEH (the basic book) has an entire chapter devoted to tradecraft in a non-game-mechanics way. To expand on that, the Faceman/Snoop has an excellent chapter on how to conduct investigations.
As for other books, you will eventually want them all. It's like a sickness. Basically, none of the books suck. But, for starters you will want:
SEH, the basic book.
SFA, the ShadowForce Archer campaign setting.
HoG, the Hand of Glory threat book. You will want the explorer, the mystic prestige classes, and the really sick gadgets they field.
Additionally, you may want:
AF, the Archer Foundation book. This contains an explanation of the Fringe, an important element of the mystic flavor in the SFA setting. It's a really cool way to add a Twilight Zone element to your game.
MAG, the Modern Arms Guide. This has detailed stats on a LOT of weapons. I mean, a LOT. As a side note, most of the later books assume that you have the MAG when writing up threats, minions, etc. But, you can get away without it.
As for your Swift character, there are two options you will want to look at very closely. The first is the mentalist psion class. This is a psion who has tapped into the awesome powers of their conscious mind. Among other things, it allows them to create technology decades ahead of what other scientific minds can even understand, let alone build.
The second is the inventor prestige class, featured in the Fixer/Pointman book (see, I told you you'd eventually want them all!). The class is based heavily on MacGuyver, but would work just as well for Tom Swift.
Oh, yeah, and the Shop book is going to have some great goodies for this character. But we're not ready to tease about that quite yet.....