1.
A maximum of 100 of each type of ampy per unit, which means the maximum boost they can give *any* girl is +3000 HP, +1000 ATK and +400 DEF. It's best to use them on your best units (6* and 5* girls), but if your favourite girl happens to be a 3*, and you want to play with her as long as she's viable to play with, then nobody is stopping you from using ampies on her. (someone on these forums did just that).
It's best to start feeding ampies at low levels, simply because it costs way less goldcoins, and the ampies provide some experience as well. But, since ampies are so rare, you will eventually end up putting ampies on high level girls anyway. More expensive, but it's still progress.

2.
Check the damage type of the whale mission you're doing, and make sure that at least 16 (preferrably more, just in case) of the girls you put on board are your best girls of that type. Also make sure that your first 2-3 teams are the best girls you have, preferrably of the weakness type, ideally also with some usefull group synergies, so the pests don't take them down.

3.
Auto set-up works, but manual setup so you get group synergies is always better. Often, using slightly weaker girls that synergize well result in a higher total output than using the "best" girls.

4.
If you can afford it, then yes. It's the same as evolving, just even better. It's just very expensive, and those elixers may be frustrating to farm.

5.
It doesn't add to the stats shown for total power, but supposedly it functions fine in practice.