I'm not seeing any water or rust in my system but have heard of guys getting it, many on this site and others. I think the best way to avoid this problem is to buy your fuel from a reputable dealer that deals in heavy volume of fuel sales ie diesel truck stops. Drain your lower fuel filter at least once a month, and use a good diesel fuel additive. I'm running Diesel Kleen, and Archoil 6200 in my 3 diesels and have had great results. Can't speak for PS 911 as never used it.
PS911 isn't a good idea to use unless you have an issue with gelling and are stuck on the side of the road... There are a lot of threads on this, but long story short... It makes the fuel burn much hotter than it should in a diesel. There is more to it than that, but I just wanted to give you a short reason.
Stanadyne seems to be one of the go to additives for 6.4's as well as archoil. I usually just use PS grey bottle during the summer and a mix of grey and white during the winter.
Change where you are filling up would be the first thing. The rust is coming from their tanks. That also means they have a good amount of water in it. Then pick a demulsifier fuel additive. As crazy said the Stanadyne Lubricity formula is a great one. So is the Archoil. I stock both here in the shop. The Stanadyne seems to work awesome on the 6.4's as far as the injector noise it cuts down. It also pulls the water out.
How much rust are we talking about btw? Enough that the filter is covered in it, or just a small amount in the bottom of the housing. It isn't uncommon if you happen to get the bottom of the barrel during your fill up to get some trash. If the filter is full of rust tho then I would recommend dropping the tank to clean it out and start over.
And, watch your rail pressure... Usually the filters will catch most of that crap, but if you end up with any signs that the hpfp could be failing, get her into a shop. As long as you aren't finding straight metal shavings in the filters you shouldn't worry too much. Like Toren said, if there is a lot of rust drop the tank and clean her up. Then do a few early filter changes (both upper and lower) and don't worry. Always make sure you are filling up from a station that gets a lot of diesel traffic.
Stanadyne is what I have been using as of late and it seems to work out just fine. I used to use Power Service Diesel Kleen as well and never had any issues.
Demulsifires pull the water from the fuel so the water separator can capture it so you can drain it to get rid of it.
Emulsifires allow the water to be mixed into the fuel so it can be burned. This is a bad thing because then you still have the water going through the fuel system and capable of sitting in things like HPFP's and injectors where when the engine is not running the water can work its magic and rust things.
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