oh god you should have posted earlier.
if you haven't done so already, update the motherboard firmware to the latest revision. X79 natively uses the RSTe ROM, at least my RIVE does. I'm not an expert on the difference, but I do know that the driver suites are different so pick one and stick with it.
Do not use the ASMedia 1061 ports for ANYTHING except traditional ATA hard drives that you do not plan on booting from. Do not attach ATAPI devices such as DVD drives or BluRay drives or SSDs to the ASMedia controller. If you're not planning on using the eSATA ports for hotswapping, you can disable the ASMedia OPROM. If you're planning on using neither the eSATA ports nor the ASMedia SATA-III ports, disable it completely. The newer ASMedia drivers seem to solve the slow boot, but they're not natively shipped with Windows 7 and will need to be updated manually.
As a side note, most X79 motherboards have additional power connectors to provide additional current to the unbuffered DIMMs and PCIe slots. Make sure that these are connected.