The lower receiver does not have to have any special engraving on it for building a pistol. It is already serial numbered and that number is on the FFL's books. It doesn't matter if you build a pistol or a rifle at that point. The only thing that would complicate things would be if you had a pistol upper on it and then put on a shoulder stock (that makes it a SBR and you would have to do the NFA forms to make it legal).
He also stated that you do not have to have a letter of certification from the manufacturer stating that it is for a pistol because of the generic nature of AR lowers. The only time you have to engrave the lower is if you are making a SBR.
He told me that the BATFE realizes that people like to change their AR's into different configurations and there is not a problem with that as long as they meet all the regs. The example he gave me was that if someone has a AR pistol and wants to add a rifle upper he can but he better to be ready to prove that he never puts the pistol upper on it when the stock is attached. He said that this could be tough to do so he recommends not to try, just too much to worry about. He also said that if you sell the pistol upper there is nothing that forbids you from putting a rifle upper on it.
Bottom line is that if you have a lower it can be made into a pistol or rifle with no special engraving needed (other than SBR). If you want to have multiple AR's in the house in both pistol and rifle, you make sure that you NEVER put the pistol upper on a stocked lower.
I guess I am good to go