Good questions and I think most of the answers you get will be personal opinion rather than biblical standards.. meaning.. nothing is written in stone.
First off, if you go fowlr, why do you want a refugium, and if you do want to keep a refugium having it in the sump isn't the best place for it. Thats just my opinion. A refugium should be above the tank so the outflow can bring pods etc... back to the tank with out the sheering action of a pump killing a large number of them. The only down side to having the skimmer out side the sump is the potential for leaks... thats all I can think of anyway.
3 Fluorescents will do well for coraline algae especially if you have at least 1 that is actinic... in my opinion coraline algae grows best under actinic and lower light rather than under intense light.
For eliminating air bubbles in your tank, you can try to control the amount of air going into your skimmer OR you can run your skimmer out flow through some carbon...The idea of a micron bag is interesting.. you would need to clean it often I would imagine or replace it.
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