You couldn't have picked a better person to do a custom build. In addition to being a highly skilled luthier, he's one of the most genuine people with whom I've had the pleasure of working.
As far as advice is concerned, I find that it's difficult to give in situations like this, as no two people's personalities are the same, nor are two custom guitars. I would say that it's best to really think long and hard about the options that you want. It gets very frustrating and confusing for the artist and the customer when specs are constantly changing. Miscommunication can lead to irreversible changes. I had it on a custom build with another luthier. Sure, it's a work in progress and some ideas will evolve as the process progresses, but if you're all over the map from the start, it may not be as pleasant an experience as it should be.
As you eluded, Scott's ability to craft a special neck is amazing. I thought about giving him dimensions, but I really didn't have an absolute favorite, so I asked that he simply carve his standard. It's by far my favorite neck and is like a combination of one of my Alembics and R9 Les Pauls.
Good luck with the build and enjoy the ride!