Caliber, you're not the only one. My group and I had a very successful Con-X campaing that ran for 2 years, and it still reigns as one of the greates campaigns we've ever played. Just about a year ago, we decided that we wanted to bring back our old Con-X cell for a 'reunion' mission (one player has since moved away, and was going to be back in town), and felt that it would be a good way to introduce d20 Modern to that player, since the rest of us were now very fond of it. We ended up running fast and loose with the conversions and the session itself, and had a tremendous time with it, but when we were done we definitely felt that there was something missing.
I think you will find that even if you manage to get a viable conversion, there is one thing that will stick out - the combat system, especially concerning Martial Arts. We really enjoyed the way Con-X combats flowed, and this was in large part due to the system of Diff levels and their resolution. We also really enjoyed the system of combos. Where else could you step up to the bad guy and say "ok, for my attack I'll execute my punch, punch, grab, break combo..." and then procede to punch the guy twice, then grab his arm and break it!! The beauty of this obviously was that it all went off the Diff of the manuever, so anything with a Diff less than your skill (or was it equal and less) was an automatic success, so if a guy with MA 4 tries the punch-punch-grab-break and the Diffs are 2-2-3-4, then the punches auto hit, the grab is automatic, and I think the break you needed to roll 7 or under? But I'm not telling you anything you don't already know - what I'm trying to say is that we only got PART of the Con-X experience, but it just wasn't quite the same. We ended up trying to write our own Martial Arts combat system that used combos, and it's been a tough haul. Anyway, good luck with your conversion!