Hi Brendon, we have 3 ponds, including one big one in Oxfordshire, England, in heavy clay soil. We were told that it would take 2 years for it to settle and clear - in fact it took 3 years, but it is now really clear. We have a stream running into the pond, so oxygen supply is good - previous posts about that are essential advice (a fountain or stream would be great). What we did to help our pond settle included adding lots and lots of oxygenating plants, marginal plants, and even adding watercress in the stream and around the pond margin (watercress vacuums up nitrates).
If you add fish (and leave it for a couple of months before you do) you should make sure that if the pond freezes over, there is an area of unfrozen surface to allow gas exchange/escape, or your fish might die from poisoning. It's easy to do, you can pour boiling water onto the ice, or simply leave one or two beach balls on the pond surface so there are spaces from which the toxic gases can escape. But don't break ice with a hammer or similar, the noise can kill fish from shock. If you do that, the ice per se will not be a problem for the fish.
Another thing - if you dug your pond to a 4 foot depth, you should expect it to drop quite a bit further -- our pond was four and a half feet at its deepest when first installed, but the weight of the water resulted in a drop of almost one and a half feet, so now we cannot wade out to the middle without an underwater swim!
