Biggest tip I wish I had known when first starting out gathering was to learn to investigate what to gather to make it worth your time. Target things used in end game crafts which the end game crafter may be too lazy to go gather for themselves. For example Silver Ore(lvl 25 node) and Electrum Ore(lvl 45 node) are used in a number of end game crafts currently. There are other things besides these too you can gather that may be more profitable and I'd highly suggest checking out something like Garland Tools pick a few things and then consult your MB to see if its worth your time to gather as prices are going to fluctuate from moment to moment and server to server.

To answer the other questions directly...

1 & 2) 99 per stack is what I did. Would gather 5 stacks worth to list as well.
3)I don't really think it matters tbh. I'd just pick one city. Someone else correct me if I'm wrong.
4) Completely subjective. I used to make a million gil a day just from gathering, but I don't think that is realistic right now because the markets are on the low side because its right before the next expansion. Prices will go up again once ShB is released and the new materials to gather will be sky high for a little while before becoming stable.
5) I keep them all on one retainer to make it easier to keep track of everything.