I played (or tried to play) in a game like this back on the Wizards forums when they were still good...it didn't end well. We barely got past the first encounter before people just stopped posting.
It's a great idea in theory...and I don't mind to knock your imagination. I just hope you know what you're getting into.
Really fun FPS' though, and that's coming from a person who typically hates FPS'.
Anyway...in response to your question. I recommend using TU's along with sort of a "Gray Wealth" system. You can treat Roubles as TU's as well, if you like, since some people treat Roubles very openly and welcomely while others would much rather just have two magazines of ammunition.
Any way you slice it; it's a tough call...and as the GM, you're the one who gets the final say. As I recall, our GM tried to use Roubles like gold pieces with other gear using TU's. It was interesting...but I would have preferred a more simple system. ^^ If you need players, I may be interested in giving it a second whack. I had nothing against the game and how it was panning out...it just died.
As for Anomalies, Traps are a solid way to represent them. Though to be fair (especially with how overpowered some anomalies are) I would recommend allowing Search checks for them without actively searching...that is...as someone is stumbling upon an anomaly grouping and they don't have a scanner out, at least give them a Search check before they walk right into a Butcher or something like that. Yikes. Though if I recall from the games, Anomalies weren't all that hard to spot to begin with. Especially the more deadly ones.