I just bought Scrivener a little while back and I’m using it to work the rough spots out of an old project. I have an old NaNoWriMo project from 2009 that I wrote using Open Office and I’m using Scrivener to start editing it to see if I can get it into a publishable format. So far I’ve got the text imported and have split it into scenes (52 of them surprisingly enough) which I have bundled up into 13 chapters. Next I plan to go back through and write a synopsis of the scenes so I can check for any plot holes in the storyline as it stands now as well as fleshing out the bios of my characters so I can make sure they won’t seem like talking heads and I can keep their descriptions consistent, as well as making any notes to rework the plot. After that I’ll go back through and write the 2nd draft.
Sounds like a great plan! Both my published (well, one published and one coming out later this month) novels started out as NaNoWriMo drafts that I rewrote with the help of Scrivener. Admittedly I often resort to physical index cards - the switch to something tangible engages different areas of the brain and feels more like playing than work 
I find that all the metadata - labels, tags and so on - are great for helping me visualise the pace of the novel. For example you can use coloured tags on a scale of blue/green (calm and quiet) through to red (high action) to chart the rising tension in your plot…
Have I missed something? I also like to work with physical index cards. I like your idea that their tactile nature may engage a different part of the brain. But my understanding is that Scrivener (at least the Windows version) doesn’t allow printing the index cards. (I really wish it did.) Is my understanding correct? Thanks. 
If you want to try printing out index cards from Scrivener, you’ll need to try out the current public beta. With that, you can create a corkboard and then print the cards off of it in 3x5 format. Let us know in the beta forum if you run into any issues!