One thing I'd like to add, assuming the financials work out and everyone is happy, is that moving from CS/programming to a CTO position is going to require quite a different skillset. You probably won't be programming all the time, at least not after whatever project they have in mind is in a stable place. You will potentially be responsible for reporting/BI/analytics, systems architecture and administration, tech support (Yes, everyone is going to ask you for help with their computers), and anything else tech-related that comes up along the way. If you want to stay in good shape as a programmer, you'll be responsible to find the focused time to code, keeping your skills sharp and current, and staying motivated to do so. At this time, you'd normally go work with an established development team who can guide and mentor you, as well as balance the team so that you have time and resources with which to further your skills.
The only thing in your post that makes me think this may be a good opportunity to explore is when you mention entrepreneurship as your long-term goal. This is likely going to be a great crash-course in how difficult that can be. My advice, though, would be to get great at what you know and learned, spend a couple years on a great dev team, save some money, and I bet there will still be opportunities for you to get into a startup for all or mostly equity.
Hope this helps. I'm just a young guy who's seen some different sides of the equation.