With the later firmware versions, doing a timed spectrum from the AP will also cause the SMs to do spectrums while the AP isn't broadcasting, so you can get spectrums for an entire sector in one go. In this case, the spectrum from the AP side is where you need to look.
OFDM equipment is very finicky about alignment. If the usual methods of aligning an AM don't work, you may have to use 5 second link capacities in between small adjustments until you get the best spot. Metrics like RSSI and S/N can lie to you, capacity is ultimately what matters.
I also find that vertical alignment can be a big deal when dealing with uplink issues. A little bit of vertical uptilt can make a huge difference.