True HD isn't necessary since this will end up as a DVD. 720x480 should be good as long as it's pretty clean (near DVD quality).
The problem with the capper scene's releases is they tend to lower the resolution to improve compression.
(Though I don't expect to be blown away by the quality from the rough cut.)
Thinking this over it'll take some restraint while editing (and possibly some OTHER episodes).
The final cut is likely to have footage (and voice overs) not in the rough cut (not just fx) because of changes made to fit continuity. They probably shouldn't be used.
I also suspect some scenes from the original version might have been relocated to other episodes to help introduce characters you would know if the pilot aired intact.
Also, the whole thing with Three-Eye/Third-Eye was in the original novel (though differently and I don't know if it was planned for the pilot).
Morgan should be introduced as watching him for breaking one of the Laws of Magic, we probably would have gotten an explanation of Bob here, and he should meet Bianca for the first time in the pilot.
Any edit will probably have to restrict itself to just replacing footage with cleaner footage and finished fx and not adding anything new.
Just my thoughts.