An update:
I loosened the allen screws on the poly top, 1/2 turn each and that took some tension off the base and flattened it out a bit. No, it doesn't leak.
I lapped the base with wet-dry paper, 230 to 600 grit. I mounted it with a fresh coat of artic alumina (a new tube). The whole job resulted in load temps 2C cooler.
I also replaced the tubing...no more brown.
I noticed that my water temps with the pump running but the PC/fans off are quite a bit over ambient. It may account for most of my water/air gradient. More data later.