sounds like you just answered your own question haha but I do want to advise you to work with a smaller case since the 1000D required a lot of parts, so since you haven't build in a while, it may overwhelm and make the whole experience more troublesome than merit.
But that's just my opinion. The 500D is also a good alternative.
with the glass so close, literally just sit right on top of those fan, you are NOT getting any air if you are doing intake. If you have those fans configured as exhaust up top, they are just heating the glass...
Whatever float your boat i guess.
Let's clarify a few things first:
1. In iCUE, did you setup the case fans by themselves?
2. in iCUE did you set up the fans that came with cooler by themselves?
3. What do you see in iCUE? Some screenshot would be nice.