Your new build is nearly identical to what i built a few months ago! Same motherboard and a similar process and number of drives. I kept my stock heatsink, while it's the only fan I hear, it's not bad at all. No issues with temps either. I also replaced all my case fans with much quieter fans, though the Supermicro fan headers don't like the low fan speed and kept revving them up and down. To fix it you have to manually lower the minimum fan speed of the fans.
I just added a mellanox Connectx-2 10Gb network card to the build and a one on my workstation. this thing flies!