1. No matter, either end first, but see #2
2. When you disconnect line at pump, either in or out, you'll drain the tank.. turn off the valve under the tank if you have one, otherwise drain the tank or find a way to stop the flow out of it.
3. Correct, no Teflon tape on flare fittings. Teflon only on tapered pipe fittings, and I prefer the goop kind and not the tape.
Grigg