Yes, I know the feeling - over 700 mods when I finally made the change, had spent quite a bit of time lurking on the Nexus to check for updates to my favorites. Most mods carried over, I lost tk's Ultimate Dragons, and a few other mods (esp. graphics) that just weren't up to par after the upgrade - better options showed up (now over 1000 plugins), and bugfix mods required the more recent game version. Then, about 2 weeks after I made the change, the 1.6.640 version came out (ARRRGGGGHHH!), and I haven't changed over to that yet.
More unsolicited advice - something will eventually break, start making a list now, and checking for updates and alternatives. Just invest the time over the next few months, break things down, so you won't have such a hill to climb should disaster strike...