I have a 50D, 5D and a 1Dmk2. I'd consider upgrading to a 1DMk2N in preference to a 1dMk3. The Mk2N was supposed to be quite a significant upgrade in terms of handling but not in IQ, so if you can live with a Mk2 it might be a better option than a Mk2N. Mk2 's are getting a liitle long in the tooth now. Having said that I love mine, big brick outhouse that it is and is my tool of choice if the conditions are the slightest demanding. Once you have used a pro body you'll find it very hard to use anything else. For ultimate IQ obviously the 5D is the way to go, just depends what you want to upgrade for.
Budegt for a flash gun too as neither have a pop-up one. Not sure what PC operating system the 1DMk2 (or N) will now work with i.e. you're running the latest version of windows it might be worth checking. Some of the custom functions can only be used/changed via Firewire, never got it to work on my PC/Camera, lots of stories regarding that "failure", not sure if that affects the Mk2N though.
Matt