Thanks for all of the advice guys!
I'm familiar with Moyer. I bought their tune up kit before I even started trying to get the A4 running.
I'm pretty sure the tank is about empty because when I pumped the primer it is sucking air. Their might be a little residual water/gas in there but it can't be much.
If the ethanol is disolving into the water, why can't it just run through it? Sure ethanol requires a vastly different A/F but shouldn't it be able to run though a few bits of it?
I'm thinking that my best bet right now is to drain the bowl of the carb and all fuel lines after the separator so I can be sure that only clean gas is going to make it to the engine.
I believe the source of the water is from where a PO tried to install a fuel line to supply an outboard if installed. The line goes right back to the tank and looks suspicious to me. I intend on removing this line as I can't imagine it is to "code" and it is just an added liability for problems.
As for the fuel water sep, it has drains on the bottom to purge the water out of it. When running I did see some water accumulating in there (definitely enough to cause serious stumbling) so, as instructed, this should be checked periodically.
I plan on picking her up this coming weekend. For the trip home I am going to use a portable tank that I know is clean. Once she is home I will tackle this job right away. I think popping the tp hatch off of the tank for a visual inspection of it's condition and contents would be a worthwhile endeavor.
Thanks again for the advice guys!