I have used both downdraft and tower coolers, and there didn't seem to be much difference between them, probably I suspect because overall system airflow is more important that a potentially higher degree of cooling applied to one area of the motherboard.
The Noctua NH-D14 (with one fan removed) is my choice for a heatsink...
If you're going to do that then you could look at the SilverStone Heligon HE01
which will give you closer to NH-D14 performance from a single fan. That's because the Silverstone fan is 38mm thick. It has a manual switch that allows a Quiet PWM range of 500 to 1200. From Newegg it costs around $75 against $80 or so for the NH-D14.
I don't know your particular Intel motherboard but I guess it will be the usual deal with a PWM CPU fan header that only runs 3 pin fans at full speed. So the PWM fan in the HE01 could be a better fit given the processor involved here. It could also make sense to use a PWM fan chain of intake, CPU and exhaust. For the additional PWM intake and exhaust fans you might consider the Noctua NF-P12 PWM
. These fans have a 300 to 1300 speed range. Yes they are around $20 each but they do come with rubber mounts, a PWM Y cable and PWM extension cable so it would be straightforward to chain them to a CPU PWM fan without any additional components or expense. The 3 pin exhaust fan supplied with the case could be redeployed as an additional intake fan. If plugged into the 3 pin fan header on your motherboard there would be a degree of thermal control to supplement what a PWM chain could provide.