Don't use them together, as they certainly conflict. Just use AV Uncapper. nGCD just allows for taking advantage of the uncapped values. It doesn't care how they're uncapped, so both will work with it just fine.
This is correct. AV Uncapper can do everything Elys' Uncapper does, although there are some differences in the way it handles spell cost for magic skills > 100. If you do decide to switch to AV Uncapper, you will need to either activate the included "example" esp file or install and configure http://tesnexus.com/downloads/file.php?id=35675. This is because AV Uncapper doesn't actually uncap anything unless instructed to by an esp file.
Which ever one you have loading last in your load order will take precedence.
No. This is wrong. Ely's Uncapper and AV Uncapper are
OBSE plugins, not esp mod files. Installing them both will probably cause a CTD (if you're lucky) or bizarre and buggy gameplay (if you're unlucky).