David--
First, I'm totally jealous that you get 6' of water from 3" of rain; I get about 3.5:1 in our pond. On the other hand, you're sure going to be shedding a lot of water in hard rains after it's full; keep a mightly close eye on downstream conditions, because you're going to have a whale of a lot of hydraulic force coming out of the overflow pipe (which you didn't mention, unless I missed something; how is it configured?)
Anyway. Muddy water in clay-bottom ponds can be a real challenge in terms of water clarity. In some cases (like ours), the clay became negatively (??) ionized, resulting in turbidity--clay suspended in the water in such fine particles that it will not settle out. After two years, I applied filter alum to the pond, the effect of which is to flocculate (clump) the clay so that it can settle out. The result was good visibility, after which it reverted somewhat; visibility is now about 2'. Too much visibility, however, and Katie-bar-the-door on bottom growth and algae; the deeper the sun can penetrate, the more stuff can grow. However, I wouldn't think about doing anything for awhile, for a couple of reasons. The bottom of the pond, if it's like ours, will be complete soup for awhile until the clay gets packed down (I think by the weight of the water--anybody know?).
If and when you decide that alum application is necessary, the source I used for filter alum is Aquatic Control in Seymour Indiana, 8000-753-LAKE. I used a stock tank to dissolve it and broadcast it with a small gas pump.
Next, you haven't mentioned aeration. Especially, but not only, in a stocked pond, aeration is critical, especially in summer. Without it, the water will stratify, with oxygen-depleted water at the bottom (resulting from the decay of organic matter, which consumes dissolved O2), and the water at the top will maintain a measure of oxygen because of atmospheric contact. As a result, fish populations must live at the surface, and the bottom of the pond becomes dead. Under certain conditions--for example, a hard summer rain--the pond can "turn over"--the exygenated air at the top, which is warm, becomes mixed with cold rain and sinks to the bottom. The "dead" water at the bottom comes to the surface. The fish die in the dead water. This happened to a friend of mine a couple of years ago. Like Bill Carlson, we use an aerator with a stone diffuser at the bottom; we also have a waterfall which contributes somewhat to aeration.
As to a dock, we built a floating dock instead of a fixed pier. It rises and falls with water level; we were down about 14" during the drought last year, so the floater was good for swimming. Also, we can cast it loose and pole it around the pond when we want. /forums/images/graemlins/cool.gif
As to fish structures, there is a hot-tub store near here and I grabbed some pallets off their "free" pile and submerged them to provide spawning grounds. This is a pretty standard approach.
Links follow to articles on the aerator and suspended-clay turbidity. You might also look at the
Farm Pond Discussion Forum, which is run by the Purdue Ag department.
Farm pond turbidity
Aerators
Have fun!!