i wouldn't be surprised n56u is yielding a better result than ac66u if your n56u is already in router mode prior to the swap to ac66u from AP mode.
I am wondering if you did reboot your ac66u after the change of operation mode to router mode, and that you have rebooted all the equipment sequentially?
I personally have not used ac66u before so i can't comment on its performance, but on paper it looks decent in terms of specs sheet.
I realise a phenomenon regarding the routers and ONTs, whenever you add a new equipment into the network, you have to sequentially reboot the equipments if the newly added equipment is after the ONT and before the APs. On the contrary, if you add anything behind the router/ap, you don't have to reboot whatever is in front if otherwise normal.
Cant really explain the reason though, I tried multiple routers before with ac828/ac5300/c5400 as routers between ONT and APs, i did have similar lower speed results. You can choose to wait a while longer to see if your speed returns to normal, otherwise if you are as inpatient as me, just reboot everything lor..