Merlin when you released the first firmware after ASUS correcting issue started to work like ASUS official, but then you have done is rolled back for N66u wireless drivers(as i remember 3.0.0.4.372.30 (5-July-2013)) and then started these lags that has been continued ever since. All my cables is fine. On official firmware i not have this issue. It's sad really ... These lags/pings may not appear immediately but after router work enough.
The driver was only rolled back for the RT-N66U. You have an RT-AC66U. Two completely different things.
Beside, the issue wasn't even with the drivers, but with the kernel.
And once again, I cannot reproduce the issue, and no one else so far either. The issue is definitely not with the FW.