I've flashed both, the 88u and 3100. After flashing, on both, I logged in via SSH and ran mtd-erase2 nvram. I then powered down both units, unplugged, powered on to cycle juice out of the caps, etc, plugged back, and booted.
I was not able to access the GUI (like others), so I did a hard reset on the 88u. When it came back up, I was able to log in to the GUI. Once in, I reset once more (clicking on the check to initialize all the partitions), and it came up fine. I configured the 88u as my router and setup my normal stuff.
I tried detecting the 3100 for a mesh node, but not able too. I plugged the 3100 directly into my laptop. It got an IP and I logged into the router which came up with the "Welcome to RT-AC-3100" splash screen. I configured it as a router, and was able to access the GUI on it. Once more, I reset the 3100 from the GUI, making sure to check the "initialize partitions" box as well. It reboots and reset. Still can't detect it as a node. I'm going to log into the 3100 as well to have a look around and see if I can find any issues.
This isn't my first go around with these, so I'm well aware of the what's normally needed during a FW upgrade. There's another user on here having the same issue with his 3100 as well.