Hi John,
1) we've been clamouring for this multi-cycle feature and I believe it is under consideration, but keep breathing for the time being
2) You can post the file and then you can do the job sheet sequentially. I don't quite understand your question. If you rearrange your processes in the NC manager, then you'll need to print up a new job sheet, of course.
3) AFAIK, you can only edit the Tool library inside the program, because it is saved in some kind of binary format eg., nctools_inch.bin if you are working in inch units.
First you get good, then you get fast. Then grouchiness sets in.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)