Regarding distance and YPAO, I would still use the farther sub as the calibration point.
If you want to take advantage of YPAO, I would rerun it if you are adding a new sub (personally I wouldn't use YPAO at all).
As for gain level, you should try to level match the subs. Use your SPL meter app and adjust them so that they have roughly the same output at your listening position, and then run YPAO if you must.
The port doesn't need much room from nearby surfaces. Six inches is plenty of room for the port.
If you run YPAO with the other sub on, it will make a new curve. The new curve should factor in both subs, so it should still be addressing the existing acoustic problems with your PB12-NSD.
If you really want a good bass response, YPAO is not the way to do it. I would get a UMIK-1 and a MiniDSP.
Here is a much superior route to getting a better bass response. I would try to avoid using YPAO.