30 days is what they said in original email: "While this pricing change will only affect a small number of merchants, you will need to login to your account and make the appropriate changes within the next 30 days."
Respect your desire and need to price accordingly. I also believe you need to respect the need for current clients that had certain expectations (a bootstrappable billing service that starts at $0).
If you are not going to grandfather the old prices, at lease give a long transition period. I would suggest six months given that this is a service that requires integration and customer interaction.
Price increase from $0 to $39 without a long transition period still does not work. If this came out at the start of the day, the outcry would've been same as $99. Feels different with the "change" but don't be fooled.
This is the evil next business model: Free "bait and switch". Get businesses to sign up with a service that is free but requires integration. Then start charging. Integration makes it very difficult to switch.
Chargify can charge what it wants, but the pricing change was abrupt and BIG. Apps on the ground floor went from FREE to $1200/year. No grandfathering, 30 days to accept. For a service that needs to be integrated, that's a terrible move that shows no respect for startups.