the roof fans are sucking too much cold air out, you want that valuable cold air going over the MOBO and out through the Rad ONLY, you've got it coming in and going strait out the roof..... those roof fans ( noctura ?) look more powerful than the rad ones..so this is even worst, you have got a dead zone where the Rad is, especially from the exhaust fan over the top of it
in addition, your front intake is blocked by all those drive bays.... no no no
you need to block off the top fans or better still remove them....block off the hole.... move that stuff away from the intake.....beef up the fans on the rad, use the spare noctura roof fans.
the side window ``in `` 140mm might be ok, just slow it down slightly, you now have only one exhaust.... exactly, this is the only place the cold air can go, strait through your rad where you want it..... not split 70:30 through the roof