So I ran three model configurations over the weekend.
1. A new "base case" model with the humidity field fixed (NDBC+quikscat winds, monthly cloud averages for shortwave forcing, etc);
2. A run with a 170m-deep flat bottom to assess how important the very shallow regions of the lake are;
3. A run with a small amount of precipitation turned on, constant, as a sensitivity check.
The results look remarkably similar, so I'm only going to show the results for the third test (rain) and mention some distinctions:

The top plot shows the average and maximum ice thickness (I don't account for open ares of the lake here- I simply divide the total volume by total area of ice.). This is still bad- we're seeing some ice hold on until the end of June, which is unrealistic. I'm still not sure why ice is sticking around so long.
The second plot shows the total areal extend of ice during the run (this is 2008 forcing, BTW). This is actually pretty encouraging. Though it lasts very late, the total area maxes out at around 50% of the total lake area (the solid line on top, about 8x10^10m2). This is in line with observations. I haven't actually seen any ice estimates for 2008 but it's something worth looking for.
The third shows the ice volume. I don't know of any way observationally to verify this or even to see if it is in the ballpark.
The fourth plot shows "heat content" relative to 0C of the entire lake. There are two curves plotted: the change in heat content due to change in water temperature, and that plus the heat change due to the latent heat of fusion needed to freeze ice. The two curves are VERY close to each other- only in March can you really discern a difference. This is really interesting, and I think un- or under-appreciated. The "negative thermal storage" of the ice is essentially trivial compared to the amount of heat that goes into changing the temperature of the water. I guess this makes sense since there's only O(0.1m) of ice but O(100m) of liquid water. Still, very interesting. It implies that ice plays a very minor role in the uptake of heat, but may play a very significant role in the heat balance by shutting down the shortwave flux. I'm going to run an identical model with the ice model turned off and compare the two.
By the way, the heat content shown here is very much in line with observations (both from the Werne/Austin mooring and from the GLENDA data).
My suspicion on the thickness of ice and the lateness of ice is that wind forcing is still nowhere near strong enough. It's clear comparing model results with moored results that we're not mixing cold water down far enough in the winter. It doesn't take much more water column cooling to completely offset the formation of ice (as in the last panel). I'm going to do another model run with the wind cranked up a bit as a sensitivity study.
Oh. Comparisons: The flat bottomed run produced less ice and it went away earlier, though not dramatically so. The maximum heat content in this case in the summer was less than in the base case.
Adding precipitation caused only minor changes in ice area or volume.
jay-