This is to clarify any confusion for anyone who wishes to change their allegiance for whatever reason.
1) You CAN'T switch nations if you have a Rank Mission active. If you are having problems with this just check your mission log. It's quite possible you are just missing a simple CS.
2) The amount of gil you pay to switch nations is based solely on Conquest Tally Results. You will pay more to switch to a nation that is ranked 1st than a nation that is ranked 3rd.
3) You WILL retain your previous nations rank if/when you switch back to it.
4) You WILL keep any CP gained for your previous nation, BUT those CP will be stored and unusable until you switch back.
5) You WILL lose all OP.
6) You WILL keep all key items, quests, and fame.
7) Switching nations WILL NOT affect anything from the past(MAW's, the nation you have in the past, allied notes).
8) You do not have to be concerned about your Mog House. It takes care of itself.