When you run into issues.. factory reset.. go the whole hog.. get rid of everything and start over.
Use names that are fully compatible with everything out there.. ie NOT APPLE NAMES.. so all names are short, have no spaces and are pure alphanumeric.
That simple rule helps no end.
If the Extreme is the new AC version then you must use the 6.3 utility.. make sure you upgrade to the latest.. 6.3.1 and make sure you have ipv6 turned on as Apple belatedly discovered they had made it a requirement.
http://support.apple.com/kb/TS4597
Be orderly and careful.. write down everything as you go along. Actually roaming network is the easiest to setup.. as there is literally no connection between the wireless in each unit..
So the rules.. apart from the above about naming.
1. Every unit has a different name. TC1, AE2, Ex3, whatever.. short as you can do it with enough to help you know immediately which is which.
2. All of the units except the router are in bridge mode.. start with bridge otherwise you have mulitiple units on the network at the same IP address.. and that is a no no.
3. Do each unit in complete isolation.. plug it into a computer.. name it.. bridge it.. set wireless.. all by ethernet all without any other connection. Update at the end and put it back into the network.
4. Wireless channels set to auto.. is the main point I would part ways with the instructions.. guys here generally say use auto for wireless.. IMHO.. auto is asking for trouble. Wireless is already 80% voodoo.. the less auto the less voodoo gets in your way. You decide wireless channels .. remember each unit has exactly the same wireless name.. exactly the same wireless security settings.. same password.. there is only one thing different.. wireless channel.
See http://en.wikipedia.org/wiki/List_of_WLAN_channels
There are 3 wireless channels at 2.4ghz that do not overlap.. 1, 6, 11 (ETSI can use 13).
Set each unit to one of those channels.. if you need more than 3 channels well you have too much wireless.. and will have to use mesh system.
5ghz does not have the same issue.. there are more channels and less issues due to its poor range.. just set whichever channels work for you. Remember with AC the 5ghz is important.. that is your fast connection.