I have a 96 stratos with two tanks. It's odd But the motor seems to run better idling and moving slowly when the port side tank is used. Any thoughts?

are both tanks going through a fuel water separator? 

Take out or replace the anti-siphon valve in the bad tank and make sure you are not sucking air in the fuel line from it. May also have something going on in the selector valve.

are both tanks going through a fuel water separator?

How can I tell?

Each tank should have a line from the tank to the switching switching valve. A single line goes from from the switching valve to the engine,. The primer bulb and any filters/separators will be in the line between the valve and the motor. So, if it is only having a problem on one tank, it has to be I with the tank, the tank line or the switching valve.

Like I said, the anti-siphon valves are notorious for causing fuel delivery problems so my first action would be to swap it out for a plain barbed fitting. This valve is the fitting the fuel line connects to. If you check, you will find there is a check ball inside that sticks and causes problems, unless someone has already swapped it out.

Thx! I'll see what I can find.

your  line to your engine would go through something like this. the reason i ask is if you dont you could have water/contaminants in one and not in the other. especially if you run ethanol gas. 

Thx. I have to run ethanol due to the distance to a non eth station.

could be a issue if you always empty the same tank and then swap over and only use a portion of the second every time.