Best way to provide clock signals for a low input voltage charge pump
I'd consider using a boost regulator to take you to a voltage suitable for your micro. For instance: -



All the devices above can produce 5V AFAIK and once you have your micro running you can drive the charge pump circuit.

Finding a booster that works from about 1V and takes you to 7V is a little tricky, that's why I opted for this method.