1. the most likely cause is that your system was installed with the SATA controller in IDE mode, and the new board has defaulted to AHCI. Change it to IDE and see what happens, that should resolve your issue. Make sure your HDD is on an Intel port, too, not an add-on like Marvell or Asmedia.
2. I find with those LCLC setups it's best to use a Molex to fan adapter for the pump, to make sure the pump gets the voltage it needs and the board doesn't try and slow it down by regulating the voltage - this makes the pump not work properly and can actually damage the pump too. Try that if possible, and plug the fan in anywhere you please, and let us know what your temperatures are like. Do you hear the pump start up and vibrate as normal?