Make a cheese sauce that doesn't go solid when cooled
Your sauce is thickening up too much because it's losing moisture. After you cook your cheese sauce to perfection and mix it in with your pasta 2 things are happening:


The sauce loses moisture due to evaporation. It's hot, and even with the lid on you will still lose moisture
The pasta will soak up water from the sauce. It's just starch, and starch sponges water up. After being mixed together the pasta will continue to soften by pulling water from the sauce


The solution is easy - add more water to replace the lost moisture while it is still warm. When I make this sort of thing I let it cool somewhat and then add pasta water in small amounts until I get a slacker sauce, then I refrigerate or freeze it. Once you get the idea of how much extra moisture you need you can add some of it to the sauce to begin with, but reserve a bit for after cooking as changes in pasta types and how done it is makes a difference in how much the pasta will soak up. 

I have also had some success in rehydrating too thick mac and cheese by reheating it partially mixing some water or milk in, letting it sit a couple of minutes, then reheating the rest of the way slowly.