Why isn't my homemade yogurt smooth? Last week I successfully made my own greek yogurt! I was and am very excited that I finally got it to work. But now the problem is, the yogurt I am making is just not very smooth. Store bought greek yogurt (such as Dannon Oikos and Fage) is silky smooth, thick and creamy. This texture is one of the biggest reasons I enjoy it so much.

My DIY greek yogurt has a rough consistency closer to ricotta cheese. It also has very small (1 mm) cottage cheese like curds in it. I found out that you can make Ricotta simply by heating up whey. That causes the albumin protein to turn into ricotta. The first step to make Greek Yogurt is to heat up the milk to denature albumin protein. Apparently this results in the protein staying in the  yogurt instead of the whey. So I thought if I didn’t heat the milk up as hot, it would keep more albumin protein in the whey and the result would be a smoother yogurt, and a higher yield of ricotta from the whey. What I ended up with was  more whey and less yogurt. More importantly, the yogurt had the same texture as before. 

Does anyone know of something I can change in the yogurt making process that leads to a more silky smooth consistency?
You are correct that the milk is heated to denature the albumin so that it becomes part of the structure of the yogurt instead of washing out in the whey. When distributed through the yogurt properly this protein will not cause the clumping problems you are seeing.

You shouldn't expect to make ricotta from yogurt whey- even if the milk wasn't boiled it just doesn't work well.

Most yogurt problems, including breaking and clumping, are caused by poor temperature control. Heating the milk too much during incubation, over incubating, or erratic temperatures, can all cause your bacteria to misbehave. Often this causes the yogurt to be too acidic and to curdle which would explain your clumping.

As has been canvassed in other answers; the best yogurt incubation temperatures are between 100 - 110&deg;F (38-48&deg;C) but it seems to vary a little with the starter. The best results seem to be had from putting 110&deg;F (48&deg;C) milk in an insulated container to incubate rather than trying to use a heater.

Many yogurt recipes call for powdered milk to boost the milk protein in the mix. Another possible explanation is if you mixed it in insufficiently.