The line "ripping out all of the drainage tiles is not a viable option" might make a nice image of an obvious impossibility, but it has no basis in real life.
The large sections of the upper Midwest are ecologically the "prairie pothole" region, with a very high mean water table and many small areas of sunken ground -depressions left from glacial retreat. The tiles are very shallow, so that two guys with a trencher/backhoe could cut the tiles for an entire farm in a single day. Come the next good rain those potholes will be full.
The restoration of the pothole ecosystem can be elaborate, but need not be. Aggressive and non-native species will colonize first (some of which have become herbicide tolerant), but restoring the biodiversity can be considered a secondary and long-term goal. At least the biologists would have something to work with and the filtration can begin.
Variations of this plan have been proposed in the past 40 years as an alternative to large dams, so there is plenty of research already completed. Here's one:
"Long-term vegetation development of restored prairie pothole wetlands "
http://www.springerlink.com/content/g13q208127x524u3/Fertilizer. Well the best data I could find right now comes from 1993, some time after the nitrates infiltrated well water and started killing babies on farms. The solution was to amplify the migration off the family farm and to move the babies into the towns.
"Each year, there are 8 billion pounds more nitrogen available in farm fields than can be used by the crops growing on this land (NRC 1993)."
"Nitrate Contamination of Drinking Water"
http://www.ewg.org/reports/nitrateThe thing you have to realize here is that farmers may work the farm, but it's the bankers who run them. They say what will be planted, and how it will be fertilized. The bank hires farm managers to look at the soil tests and to see that the recommended amounts are applied. No one will risk being accused of skimping.
Anecdote: I talked to one farmer who was told by his banker that he couldn't have a horse on his farm for his kids unless he could show that it was part of a profitable breeding plan. Not uncommon. This was during the farm debt crisis of the 1980's, but as far as I know it's still true.
Animal Waste. The image of a lone farmer mucking out a barn and spreading it on a field is so old now as to be quaint. Rather, imagine a leaky lagoon full of sewage equal to the production of a medium-sized city being trucked out and dumped in a field on a single day. It is impressive enough to drive the few holdouts off the neighboring farms and into town. Farmers don't have livestock, corporations do, and they do it in multiples of 10,000 at a given location. It is not regulated as sewage would be. If they had to pay for real sewage treatment, proper wages, the full cost of the road network and trucking, and non-subsidized grain, I have my doubts as to whether the operations would be profitable and we might have better pork for the effort. Almost everyone here already knows this, but I've enjoyed typing it again.
I admit I'm not up-to-date though on the current sewage regulations or enforcement and I don't want to be. Someone else can step in, so to speak.
Riparian border. Your last question is the easiest, as I remember one study in particular, done by ISU extension in the 1980's or so showed that a simple strip of short perennial grass 2-3 meters wide was sufficient for a high filtration and soil retention. More important was the use of the grass strip upland in the watershed to control runoff. I would imagine sources for this are available from every ag uni and field extension, as it's been duplicated many times, many places.
Each step mentioned here has been known and fought over for decades now.
Should anyone be so foolish as to advocate something so rational and cost-effective it's obvious who your enemies would be: from Grassley to King to the same damn Governor, to the bankers and suppliers, to Monsanto and the meat packing plants. But you might be forgetting one of worst, Jack "the bad egg" DeCoster, (yes, that guy) who first made his big fortunes in building otherwise unwanted large hog lots in the 1980's in Iowa. He was "bullet proof" then, had layers of unseen protection, and I doubt anything has changed.