Normally, YPAO is very accurate for levels and delays (aka distances). At least in the past, it is usually not so good for crossover frequencies (i.e., "small" vs. "large" for speakers, and choice of crossover frequency for the subwoofer). Fortunately, what it is not good at is easy for people to do who know the specifications of the speakers (pick a frequency above the -3dB point of the main speakers, and select "small" for them unless they are as good at bass as your subwoofer), and what is hard for people to do manually is easy for it to do automatically. I strongly suggest either borrowing an appropriate microphone from a friend, or buying a new one from Yamaha.
And, if you want the best sound in the future, you will either need to not misplace your microphone, or you will need to keep buying a new one whenever you move any furniture in your room or move any of your speakers.
Of course, you can spend just as much to buy an SPL meter and do the whole thing manually, but that is more trouble and will likely not yield any better results. And, naturally, if you misplace the meter, you will have the same problem in the future that you have now.
