K.M.
My son did not like jarred foods. He always wanted what I was eating. However, if he couldn't chew it to the extent that he felt comfortable swallowing it, then he spit it out. You said your son was just getting molars, that he cries when he isn't able to eat something, and that you have chosen to puree food for him so that he can eat. Good for you. Let him eat his food in the manner he feels comfortable with. As he grows more teeth, he'll be able to do the work of the processor himself. In the meantime, he's eating, happily, a wide variety of healthy foods. Who would complain about that? If you remain concerned about it, try leaving the consistency a little chunkier. See how it goes.
You pediatrician has left you in a bit of a quandry regarding the whole milk. My understanding, and this is just my experience, is that whole milk isn't necessary; breastmilk is all that many humans and other species ever consume; it's just a convienent source of fat, vitamins and calories. According to the pediatric specialist I saw with my son at a feeding clinic, a child your son's age needs to be getting around 1000 calories per day, with 12-16 oz coming from whole milk, and no more than 8 oz juice (considered empty calories). Hope that helps.