Hi Evolutionary! Welcome to PBF and welcome from another fellow pond owner and pondlover in Michigan. I'm in the greater Grand Rapids area and you are welcome to stop by anytime you are in the area. I'm sure we would have a lot in common!
I can tell you have been lurking for a bit on the board, you are doing aweseome on your planning, investigating and study.
You are finding out one of the rules of this board which is that no matter what someone says your pond is for depth, spring fed etc, you need to prove it yourself. It would be very hard with most soil types encountered in michigan to have a 40 foot deep pond since you can't usually excavate with vertically steep sides.
You didn't mention the surface area size of the pond?
I see some vegetation on the bottom near shore that does not look like charra or FA. Hopefully some of that helpful vegetation will consume some of the nutrients.
Do you have water or power or both at the pond? How much water can you pump?
have the FHM spawned?
Is there a way that fertilizer run off can make it into the pond?
I'm not sure I can answer your questions about stocking since I'm still at the stage where I only have forage in my pond. I did put some rusty crayfish in this summer, some freshwater shrimp but no predators.
You already have SMB, LMB and CC so not sure how you go from here. I imagine some other apex predators would be helpful, NP, some have even mentioned pickerel.
Welcome and thanks for the awesome pictures. Those SMB look great.