First a little background on our pond:
We began construction on our pond late summer 2016. We were blessed with a dry spell that lasted for pretty much the entire excavation process. What we ended with is an approximately 3 acre pond with an average depth of 8'. The pond is pretty much all dug as we had only about 1.5' of fall over the 500'+ back stretch of the pond site. It has one corner that goes down to 16' deep and on the other side there is an island that will be submerged 2-3' at full pool. 4:1 slope on all banks and the soil was clean clay from about 2' down. Pond was dug with dirt pans.
Once the pond was completed we had small rain events beginning about a week later. I had plans to put gravel on top of the island for spawning area and SMB beds on the slopes of the island as they will see less siltation hopefully since the island is under water. I also plan to have about 6 Bald Cypress trees on the corners of the island. Before I could complete any of this however, the rain set in and the pond filled much faster than anticipated. I expected to be pumping water from a well and hoping for rain for almost a year before I saw full pool. Now, about 2 months after completion, the pond is full.
The problem with the quick filling of the pond are that I was only able to get the top couple of feet of the pond banks seeded before it filled and only a little of that actually had time to germinate. Now I'm left with very muddy water as there is exposed clay on the entire pond basin. We did a jar test and after 2 weeks undisturbed in a dark closet the water is still very cloudy.

Here is where I start to feel overwhelmed:
My hope was to stock scuds, minnows, and maybe grass shrimp this spring and give them all summer to reproduce before introducing other fish. From what I've read though, most of those critters will do much better in clear water. So now I'm thinking step one is clear up the water, but that seems almost a hopeless venture until I get vegetation around and in the pond. Problem with that is its hard to get plants to start in January. Am I just being impatient by wanting clear water so soon? Would an alum treatment be in order? I need suggestions on what sorts of vegetation I can use to stabilize by pond basin and clear up the water.

I think I would plant grasses in the runoff areas when the soil warms up enough. Lots of us have faced the same problem. A floculant would clear it now but the rains will just bring in more sediments until the grass is established. Try plain Bermuda.

Thanks Dave. That's pretty much what I had in mind, as soon as it's warm enough get grass established all around the pond, especially in runoff areas. How about in the actual pond itself? What are some good options for underwater vegetation that will help keep my clay bottom pond from always being muddy? When the jar test shows water not clearing after a couple weeks does that mean that the pond will likely not clear by just waiting and will require a floculant or is there still hope for no treatment and clearer water?

You can try but, without grasses, it will likely revert to suspended junk.

You can't do much for what is underwater. Throw rye grass seed out asap, then over seed with warm weather grass late this spring. You can/should also use hay to cover the dam, and areas all the way to the water edge, and it will help seeds, and with erosion. A limb/leaf chipper would have made this fairly easy, but I didn't know at the time. YouTube it.

Water will likely clear, but we can be pretty impatient. Mine looked exactly like yours, and filled almost the same way. I got some things done, but not nearly as much as I had wanted to before the rain hit.

http://forums.pondboss.com/ubbthreads.php?ubb=showflat&Number=431675&page=1

I used hay on the dam, and also threw alfalfa in the water. Mine was clear by spring. I don't know if the alfalfa had anything to do with it clearing or not. I did go back and rake out all the alfalfa I could after it cleared. Much harder raking out than throwing it in!

Welcome, I would also suggest that you buy the common Bermuda that is pelletized (has a small amount of clay on each seed)and put it down in the spring after the ground reaches a temperature of 70 degrees. Pelletized comes up much faster that hulled, mine came up in less than 7 days. Like Brian said I used hay to hold my seed in place and it helps to keep the ground moist. You will need to water it at least twice a day (small amounts so there is no runoff) then fertilize it later.