As much comfort and familiar with d20 as I am, I'd stick with TS/SI rules. It's simple enough to convert TSsi stats to d20, (multiply or divide by 5) but I don't think it'd be worth it. D20 Modern, IMHO, is better than Spycraft 1e, I know nothing about the later editions. Top Secret SI had a really awesome and fast combat system that I don't see translating to d20. And as a modern, real world game, did a better job at being realistic and simulation like. Unlike d20's abstract combat.
What exactly are you trying to do?