NP, I enjoy working on this chart, gives me something to do since beign rank 50 my goal is no longer SP oriented!

There is always a favored bait for each fish, with some exceptions.. Malm Kelp has no favored and it is my assumption that rare fish (Ocean Clouds and such) may not even have a favored bait. So in the case of White coral using either Goby Balls or Rat Tails is just going to make it easier to get them. Favored baits definitely do not alternate and there is no specific time for when they work.

I have no idea on the specifics of SE's system for how each fish is caught. My assumption is that each condition you mean gives you a % chance in your favor, so for instance.
  • Properly Geared Out, Appropriate Rank and Stats % Increase to hit fish at the depth you aiming at
  • Using the Favored Bait % chance to pull the specific fish that bite at that bait.

Also Note: Just because a bait is favored by a fish does not mean you will be getting that message often. For instance Crayfish favor choco flies, but personally I see that message once every 40-50 pulls of crayfish.