Long-term suspended clay (to be treated) and murky water immediately after a big rain raised the pond level 3.5 feet overnight are NOT the same thing!
I would let the pond "relax" for several days after that big rain before performing any treatments. One of the ways a fish kill occurs after a big rain is that the cold rain water on top can cause the pond to turn over and the unoxygenated bottom water is now raised to where your fish are living. Also, bringing in some organic matter can use up some more oxygen in the water column as that material is oxidized as part of the normal decay process. Finally, even a few days of heavy clouds can set back the oxygen production from the photosynthetic organisms in your pond.
If you are drawing bottom water from your pond to feed your bog system, then your pond should not have much anoxic water on the bottom, even if the rain did turn over your pond.
However, that big of a rain event was almost certainly stressful on your fish.
A portion of the current murkiness is probably some silt and some non-charged clay particles that will remain in suspension for just a few days. I do not believe a chemistry analysis performed NOW would be indicative of the "normal" state of your pond. If you want, you could take samples over the next few days and chart the changes in your pond subsequent to a big rain event. When your readings stabilize, that will be more indicative of the normal state of your pond, and you can use that information to guide your treatment plans.
Good luck on getting your fish through this stressful time! It sounds like you have put in a lot of effort to create a good pond environment for them.
