A: The mouse and tribe stats are updated once a day. The stats on CFM lag behind your actual in-game stats by 1-2 days.
A: The ratios are calculated using the total rounds played, not cheese gathered. Otherwise those that pad their stats by not entering the hole would be at an advantage.
A: The ranks are calculated by performing a normalization on each individual stat and summing these values into a composite score. Shaman saves and firsts are weighted slightly more than cheese gathered. For mice, about 80% of the rank is determined by raw stats, and 20% is determined by ratios. For tribes, about 40% is the total raw stats, 40% is the average raw stats, and 20% is the ratios.
A: If you have under 1,000 cheese gathered or less than 5 mice in your tribe, you won't be on the leaderboard. New tribes and mice aren't immediately added to the database. It may take up to 48 hours for them to show up. If you are new to the game, you can register for an account here and that will ensure you're added after the next update.
A: The tribe API is broken so your tribe members need to manually update their tribe. This can be done in-game by inviting the bot Flourdough or Flowerdough to your tribe which will update your entire tribe. Alternately, you can use "/c Cfmbot tribe" to update the tribe on just your profile.
A: A mouse's save ratio can be higher than 100% because you aren't limited to one save per round like with cheese or firsts. To get a save ratio higher than 100%, you simply need to average more saves each time you shaman than the number of rounds it took you to get to shaman (easier said than done :p).
A: Yes, bootcamps are added as a small bonus to your base ranking.