Well we are back from the vet and it is as I thought. Diagnosis unknown with a strong nod towards 'behavioral' issues. He did the regular checkup with the anal gland expression. One side hard and one side regular.
We are going to try the pheromone defuser in the living room, some extra attention to make her feel special again (she is quite possessive I am learning), and a daily sweep of the cat box area in the laundry room.
We have decided that our last resort is the additional litter box on the opposite end of the house. With the older cat fully trained and never an issue, we truly do not want to start her on a habit of using a litter box in the living room.