I don't think there's enough material available to make it into a decent miniseries, but I could look into doing 20- or 30-minute segments. They wouldn't be the exact same chapters as the graphic novel (obviously, since that would be 5 and a half hours long if each chapter was 20 to 30 minutes), but it might work.
Honestly, I don't have a problem with it being a long film - I have the near-5 hour version of Das Boot and love it to death. I may not ever watch it in one sitting, but it's still one of my favorite films of all time. (Never seen the 3.5 hour director's cut or the 2-hour US theatrical version.)
I'll look into less Nixon. No promises there (it's generally unavoidable).
Definitely more Philip Glass, I'd like to use more Dylan (I'm going to try to find a new spot for The Times They Are A-Changin' since I'm removing the credits). In re-reading the graphic novel, I've discovered that Desolation Row is quoted in the first chapter, so I'll look into placing it in that section of the film if possible. If not, so be it. It'll likely go in the credits, mainly since I can't find that John Cale song (Sanities) fucking anywhere.
Here are the Rorschach's-death-scene shots I'll likely have trouble with, and they all involve removing Dan from the image: