I don't have a positve solution, but would like to add that I built my brother almost the exact sytem I have in my sig, only diff is a 380 PSU instead of 430 and he has a combo CDRW/DVD drive and only one HD. He has this exact same problem of superlong boots, are you like getting to the desktop and taking another minute to get windows properly loaded?
I would just share some of my trouble shooting with you that didn't work so maybe you don't bang your head to death. Tried onboard sound and separate sound card, multiple OS reinstalls, different video card as well as multiple drivers, single stick of ram in multiple slots and tested both sticks with memtest, Asus and nVidia NF2 drivers, fiddled with various settings in BIOS but not power and suspend settings.
His computer didn't experience this problem after I first built it. I came to the belief it happened when he went from XP Home to Pro and that it is some kind of networking issue in windows that may or may not include his DSL modem, but at that point we didn't want to do another reinstall back to Home to find out. You may try shutting down your built in NIC's and see if that helps. Matter of fact I'm gonna recommend him to try that himself. We both have used the nVidia from day one, 3Com is disabled. Try all the combinations with the NIC's, one on/off, both on/off. Good luck!