Hi Lucas,
Welcome to PondBoss! Always great to find others in MI with a love for ponds.
It sounds like you could tell us quite a story about the joys and pains of being a pond owner. If you have time, share with us the history of your pond and what you learned over time.
For your muddy water problem, do yo know why it is muddy? Do you have a source of water that flows into or out of the pond? What is the soil like that you encountered when digging out? Did you do a complete drain, dry out, dig deeper, then refill? Was there clay there already or brought in?
I ask because soil types determine how fast the particles in the water will settle. In addition if you have fish or crayfish stirring up the bottom that can add to the turbid conditions.
There are good threads about this and Rainman is the expert on this. I tried to study those treads but the chemistry of Alum plus keeping the pH balanced is beyond what a do it yourselfer can do. You need to measure your volume of water, your pH, then calculate how to put in enough alum and then enough buffering compound to avoid a pH shift. You need a floating barge to do it right with large pumps.
But I'm sure someone can chime in and help you. When we had our pond redug, as a testimony to the typical MI ground water pond, we had little clay and very clear water for weeks after refilling.
WE have used the polymer product Soilfloc to help seal ours. It is a two part product and one part acts as a floculant (it grabs the suspended particles because of their electrical charge) and pulls them to the bottom. It does a great job of clearing up the water and then that silt and the polymer are pulled into the bottom of the pond helping seal the bottom. I don't know how long the water would stay clear since ponds with clay bottoms tend to get muddy again anytime there is a inflow of water (like a big rain with surface water runoff)
The Alum seems to last longer and someone smarter than me can probably explain why