Why isn't my homemade yogurt smooth?
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.