Hi Nick,
I'm probably the wrong person to ask in some senses but...
Bluetooth: think sideways. What do you want to connect? Is there a different way to connect it? E.g. if it's a phone, get an Aux cable to connect it to the amp.
YPAO: don't worry, YPAO isn't much use on the cheaper Yamaha amps. It takes a bit longer but put on some audio with a high dynamic range that you know well (I often use Pink Floyd - Time) and use your ears. Don't bother trying to make it "right", concentrate on making it right for you.
USB: again, it depends what you're trying to connect. Would a lot of what you want be fixed by getting a "smart" Blu-Ray player or a streaming device? E.g. if you want to watch movies off a USB stick, maybe you can stream them from your PC to the player or streaming device using Plex. (Plex is awesome and free.)
Hope this helps,
Arron