So it turns out that the "Ultimate Cut" of Watchmen (with Black Freighter cut in) is going to be 251 minutes long, which shakes out to 4 hours, 11 minutes. I'm going to try to keep my cut down below 4 hours, and am strongly considering doing an alternate cut that doesn't include Black Freighter, to keep it to a more manageable length. I feel that the film could benefit greatly from some alterations, even if Black Freighter is gone. (This version will most definitely not be called "The Graphic Novel Cut," though.)
The "Ultimate Cut" is coming out on November 3, so I expect work to start on this after the end of the semester (mid-December), seeing as how I'll be busy as hell editing stuff for school during the rest of the semester. It'll give me plenty of time to watch the UC and make a more detailed plan for changes, though.
--edit--
It appears that 251 minutes was a typo on TheDigitalBits' part - the actual runtime is 215 minutes, or 3 hours, 35 minutes. Compared with the DC's 3 hours, 6 minutes, that's 29 minutes added - Tales of the Black Freighter is 38 minutes long, so that's 9 minutes cut from TOTBF, at the very least. Bear in mind that additional footage has been added to transition to and from Black Freighter.
So I guess it's not so much a cut-and-paste job, and they're actually cutting it to make it work within the story.
And seeing as how the final run time is about 3 and a half hours, which is what I was aiming for at the maximum, I will not be doing two versions - it will be just one, with Black Freighter intact.
I think this runtime news also means that none of Under the Hood has been cut into the "Ultimate Cut," as some had speculated.