I've taken the project as far as I can, and I will shortly be handing off all materials to a few different people in hopes that they will be able to get the second disc done. The first disc has been done for a while. Somewhat fittingly, right as I was about to burn discs with the source material, my video card crapped out and that computer is out of commission for the moment. I have other discs floating around with the material on it, so it's not lost or anything, but just another setback for a project wrought with setbacks.
Sorry for the delay,
PS - the deleted scenes are from workprints, so there are lots of print damage and missing sound elements. I don't believe that a watchable extended version could be constructed.
PPS - According to Gilliam (from the book Gilliam on Gilliam), Criterion offered him the chance to make a restored cut (to the original 3+ hour running time) when the laserdisc was made, a la Brazil. This project was never started due to financial constraints (the projected cost was 250k dollars at the time) and because Gilliam was burned out at that point. Perhaps with newer digital editing equipment, the cost could now be lower. Columbia certainly doesn't seem to give a damn about it, so maybe it's obtainable.