Pricing should always be a reflection of:
- Cost of living (how much do you need to earn to live)
- The actual time spent working on the project
- Cost of doing business - like your computers, electricity, education and training, office space, etc.
- Any regulatory/tax costs that you are responsible for
Putting it all together you should end up with a good pricing structure that reflects the reality of the costs of your time and resources to accomplish a given work.
Over time you'll continue to tweak and improve your pricing structure (and your project estimation skills) until it is second nature and fairly accurate for any given project.
In your particular case I would suggest charging for the hours spent, broken down into 1/4 or 1/2 hour segments.