I don't know how you intend to handle nutrient in your hydro system, but, if you have any small pipes under pressure and pump the nutrient, manures (even teas) will cause clogs.

If you sterilize the manures/teas, you will kill the useful biota in the manure/tea.

Maybe I would have to filter particles. Anyone have any experience with using manure for hydro? Seems it would be a good natural process to help complete my ideal farm cycle.

I feel if you keep it off the parts you eat and touch, then E Coli is not so much an issue. perhaps an EnF system with a lid over the medium.
And / ot you could find a beneficial bacteria that'll overwhelm the nasty stuff.(kind of like yeast does)

primstuff
I honestly don't worry much about E Coli, I feel I do a good job of washing my produce where that is not going to be a problem. However if you want to sell what you grow, it's just about imposable to control how others process their food. I had a pdf copied to my computer that I think might be useful to you. Granted it's about growing aquaponically, but manure is manure (fish, or any other animal).

On-Farm Food Safety: Aquaponics

I haven't read it all the way through, like I said I tend to save things to my computer for later use. Although I believe it outlines the type of procedures you were looking for, and it was conducted by the University of Hawaii.

I would consider using a Bio-filter in my system, if I wanted to grow with organics/hydroponics. A bio-filter is really not much more than growing medium that beneficial microbes can breed in.