If you want 64GB RAM, go for whichever configuration is cheaper, you will only get quad channel either way.
Your chosen case will not accommodate an E-ATX motherboard. You should check the manufacturer's website for information when choosing a case.
GTX 1080ti is good and will be for a long time, if you are staying away from 4K.
The Threadripper 2990WX's talents lie in quite specific user scenarios and it is not good at running games. Do some research to make sure you get the right CPU for your needs.
Can't help you on water cooling.