First off all, congrats. You must have impressed whoever you interviewed prior to this point to get to the CTO interview. I am going to go out on a limb and say your last interview is nothing more than stroking the ego of the CTO, unless something is majorly wrong with you and you will blurt it out on this last interview in the process.
Coming back to your questions:
What can I expect?
Expect a personality characteristics driven interview rather than the techie stuff the previous interviewers put you through.
What kind of questions will I be asked?
This depends on the person interviewing you. Nobody else can tell.
How can I prepare?
There is no preparation to this other than being and acting professional
What kind of questions should I ask?
These are things come to mind but only to my mind, not an exhaustive list:
what is your biggest pain point(s) and how can I/my skills can help you get through it/them? Unless it is ovious that they are severely
understaffed and you will be expected to work from day-1
what are the short term and long term goals of the company ?
How much growth are you expecting in the next 1-2 years ?
Related to the previous question: what would be a growth plan for me in this expansion process ?
Here as a last question, I would ask something about how the company culture, but if you interviewed 2 people and it is a small company,
you may already have developed a sense for it. But if you haven't, a
soft question like that, wouldn't hurt
What are things I should not say no matter what?
Oh boy... this is a touchy subject but again, do not talk about salary, increases in salary unless you are specifically asked. Even in that case, try to deflect them with round-about answers, like negotiable, or having your performance guide them to decide what you are worth. Also, do not talk about flex schedules or working from home arrangements or any other fringe benefits that company is providing or will provide. Do not bad-mouth your previous employers, bosses or jobs/assignments. Again do not ask if you can access the internet freely from your workplace, as it is a sign of slacking off in the eyes of a supervisor. Use common sense is my best advice to you.