I don’t use Mac, so haven’t used Scriv 3 yet, but I hang out on the forums quite a bit and have a sense of where the new release is different from V2 and where it isn’t. I can address the points in your post.
It’s a major upgrade. Biggest in years. So big they have charged us for it. Things have changed. A lot.
I don’t believe the functionality of structuring things in the Binder has changed at all. For setting up your Parts and Scenes structure, have you tried simply dragging and dropping the items where you want them to be? You can drag the Parts where you want them within the Manuscript folder, then drag Scenes into the Parts. When you are done with the Parts and Scenes, click on each of your Chapters and then select Move to Trash.
If you get your Parts and Scenes into the Manuscript folder as above, and you don’t have anything in the Manuscript folder but the Parts and Scenes, your total manuscript count should be correct.
V3 Compile has changed dramatically. Read the V2 to V3 upgrade guide here:
[url]Updating from Scrivener 2 to Scrivener 3: A Guide]
Greg, if you are under a deadline, then you picked a really bad time to upgrade and just added a certain amount of stress to your life. How much stress is hard to say, but based on the relatively basic level of your questions, learning the new release while getting your manuscript out may be asking too much.
I recommend that you give yourself a defined period of time (half day? whole day?) with the new release and see if you can make it work. Go through the upgrade guide as suggested above. Don’t try this without reading the upgrade guide. Basically this a trial, to see if you think you can figure out the new version and complete your actual work.
At the end of that period, decide whether using V3 is feasible for you during this critical time.
If so, come back here with questions as challenges arise.
If not, downgrade your scrivener version to 2.9, which is the last version of the Scrivener 2 series. Your V3 license will work with 2.9. I believe you can run both V3 and V2.9 concurrently. In V3, you will need to Export your project in V2 format, to work on it in V2.9 again.
http://www.literatureandlatte.com/scrivener/release-notes?os=macOS
Another alternative is to ditch Scrivener for this round of edits and continue working in Word to meet your deliverable. What Scrivener functionality are you using to help you get through this point in your process? If you are doing a lot of reorganization of your manuscript, then the Scrivener binder will help. But if you are just going through and reviewing/incorporating/making edits, then you might be better off staying in Word at this point.
ETA: I see that Brookter had already responded while I was typing my tome, and much more succinctly! What he said!
HTH,
Jim