Speaker cable length will not matter
The idea behind having all speaker cables the same length is to attempt to ensure that the *signal* reaches each speaker at the same time. But electrons travel down the wire near the speed of light so for all intents and purposes it won't make one single bit of difference if the cables are of different lengths - cut them to the appropriate lengths to minimize the mess. The signal will arrive at each speaker at the same time.
The distance set up for receivers is to ensure that the *sound* from each speaker arrives at your ears at the same time. Sound travels ~1foot/millisecond. Neither your Yamaha, nor any other receiver, takes into account the length of the cables as it is irrelevant.
You need to measure the actual physical distance (in meters or feet) from the ideal listening position to each speaker and input those distances into the speaker distance setup in your receiver's menus. The receiver will then calculate the delay required to achive the objective of all sounds reaching your ears at approximately the same time.
Note that the delay calculation really cannot account for characteristics of your room, like when the first reflection from a nearby wall occurs, but in practice it doesn't matter anyway - even if your distances are off by a few feet you likely will not notice any difference from setting the exact distance. The absolute minimum audible delay that I have ever seen proven is 6ms (thus a distance error of 6 feet) and that is only with pure tones, not music or movie soundtracks.
YPAO and other systems like it will attempt to take into account characteristics of your room and try to eq the sound to make it 'right'. I have no experience with that, but others have said that it does a pretty good job.
Nice setup. I guess you are firmly in the 'too much is never enough' camp.