Check out
www.epa.gov/otaq/regs/fuels/rfg/waterphs.pdf
Ethanol isn't that big of an issue, but we actually have to worry about water in fuel much more now than we did before. Especially as it gets colder. Ethanol can hide a water problem at high temperatures and then bite you hard when lower temps hit. It also rusts any steel in the system and busts up the sediments in your tank and sends them through your fuel system.
Replace the seperator and fuel filter first as they're easy, but my guess is that you have carburetor blockages. Only once, in about 20 fuel system related engine problems, have I ever found a fuel filter to be clogged so much that it was causing problems. Every other time it was either a bad fuel pump or a clogged carburetor.
The one time the problem was the fuel filter, the engine wouldn't die, it would just loose power after a few seconds under load and "sputter" along.