Next on your list is look at ways to reduce the amount of rainwater reaching your horse's confinement areas. Good sites to divert clean rainwater to include a ditch, lake, creek, wetlands, rain barrel, dry well, fish pond, or undisturbed area of your pasture. Be sure to plan gutters, pipes, etc. to handle amount of rainfall for your area. Protect downspouts so animals don't destroy them. This can be done with heavy PVC, hot wire or by simply making the downspout area inaccessible to horses.
Footing is another important consideration for reducing mud.
Using some type of footing, at least in the high traffic areas, will reduce mud. This keeps the horse up out of the dirt, and allows rainwater to percolate through and drain. Hogfuel or wood chips can provide an excellent footing. These wood products offer good environmental controls as well. Through the natural composting process they contribute to the breakdown of the nitrogen in the horse's urine and manure.