You said they were "intricately intertwined." (Did you really mean "inextricably intertwined?") Either way, to say that they're "intertwined" would imply that terrorism and illegal workers are crossing for the same reasons. They're not -- and thus the manner in which you deal with the problems is different.
The border is certainly a common point between the two problems: it's good to require registration, to include a background check of some sort. One hopes that the background check will catch bad guys, but one suspects that it would be weak.
That said, the tracking problem is completely different for terrorists vs. guess workers. "Guest workers" are relatively easy to track, because they have employers, and the vast majority would really be here to work. Their off-hours are not of much concern.
Terrorists might make use of the same program, and they would probably also be "trackable" through the employment system ... but their off-hours are the part that really matters to the intel folks, and that's probably not trackable.
"If we are engaging in a WOT, allowing anybody who wants to to enter our country is ridiculous. It makes the WOT a joke."
I agree. The issue IS national security. I've noticed that some, not willing to admit that keeping an open border is not condusive to effectively fighting the WOT,simply argue that the hijackers did not cross the border. And then there is President Bush, who has just wrapped up several speeches on the WOT and addressed the nation regarding 9/11, yet I did not hear him mention the fact that the border remains unsecured.