Which FAA regulations apply to the Stratolaunch?
That would be under Title 14 CFR, Chapters 400-460.

A lot of this stuff really hasn't been finalized yet and these vehicles are considered only experimental and regulated similar to homebuilt aircraft.  Passengers are required to sign waivers advising them of their risk and that they understand this and hold the organization indemniable to any and all liabilities involved with using this system.