Is there someway of determining what enemies will provide a challenge to the PCs other than guessing based on past experience? I'm thinking of something like CR (Challenge Rating) levels in DND, where if you had a group of four adventurers at level four, then you could consult a chart to see what enemies would be best to send at them.

Surely not all elites are on the same level, nor are troops or masters, so how does one know what to send up against a Rank 2 Kill-Team? A Rank 6 Kill-Team?

There is no hard coded system to tell this. I've actually found its one of the most difficult aspects of GMing the games of the 40K RPG line. The modules do a reasonably good job of giving recommended encounter sizes, often based on things such as "one elite per PC," or that sort of thing.

Personally I've come to the place where I just sort of determine the size of the enemy force, and what it should be based on the resources available to them (the enemy that is). Then I try to have them react accordingly to the threat the PCs are making themselves out to be.

It's kind of bummer if the only way to tell how much a Kill-Team can take is through trial and error. I really hope they can write a detailed method of doing so in the future.

The answer:

A kill-team can take on as many enemies as they can take on.

"Uh?" you say?

If your players are smart, and can use their tactical and strategic assets to the best of their capabilities, do not limit themselves just to "shoot it or smack it straight up", and can come up with ways to use their environment and their enemies against themselves; then they can take on entire armies.

If however, the brightest notion your average player can come up with is to shoot them with a bigger gun… Then they'll never be able to take on any decently powerful enemies. Because, if their enemies started to use their brains and were somewhat powerful, it would probably be TPK time.