I have the same build but no gpu yet.Honestly it should last you 3 to 5 years easy if not more.My brother has a 3900x and 2080 super and he can still 1440p game at 144hz with some small settings turned down a tiny bit.
you dont need 1000 watt psu you need 750 to maybe 850 max.Thats way over kill and that money can be spent for a better video card.For your cooler the deepcool ak400 will work great and the money saved not buying a aio can be spent else where.
Micro center has the case you want https://www.microcenter.com/product/652637/lian-li-o11-air-mini-glass-version-tempered-glass-atx-mid-tower?rf=PDP_altSell+>+Cross_Sell+>+Cross+Sell+Computer+Cases+Broad
Its a micro center only case but is the air mini with a glass front on it.It takes a atx psu and all the air mini specs.
I have been doing that for 20 years with zero problems,I change out my tim every 6 months to year depending on temp change with age and i have never had too much used yet.
A custom loop will always out cool any aio made.So yes if your going to custom loop do the cpu and gpu.As far as should you water cool your 1080 or not is up to you.If your going to buy a new gpu soon id wait and watercool that one.
I do the pea size in the center and mount my cooler.I'll wait 5 mins unmount the cooler and check my coverage.If im happy with it remount the cooler if im not i add a tiny bit more and do it again.