I just installed my second Nvidia SLI configuration, and experienced the same setbacks. My first rig used dual eVGA 7800GTs, and I just upgraded to eVGA 7900GT KO Superclock models. I used the eVGA Nforce 4 SLI motherboard for both; it handles SLI a little different than the rest by having three PCI-E 16x slots. Use the middle slot if you have one video card, or the outer two if running SLI; no fussing with anything. I had one card running without issue.
After installing the second card and shuffling the first the PC refused to boot. Various screwing around did nothing for me but increase my blood pressure, so I unplugged it and left for a few hours. I plugged it back in and powered up the PC without incident. While booting I consulted the manual and found that video output is handled by the second card in SLI, which I had my monitor connected to from my previous SLI experience. Rebooting found no video signal, so I moved it to the top card. There was Windows XP, and the Nvidia drivers were letting me know I was set up for dual display, but did I want to enable SLI? I tried to enable it, but my resolution was at 800×600 and the dialog box was appearing on the second phantom monitor, which I finally right clicked around for and cleared up. I clicked through and enabled SLI, which asked for a reboot. I rebooted, but only after moving the monitor to the second video card as the manual stated. Rebooting brought me to another blank screen, so I swapped again and found the Nvidia driver asking me if I wanted to enable SLI.
After recovering from my overwhelming deja vu I clicked through and rebooted. This time I left the monitor where it was and of course rebooted to a blank screen so I moved the monitor to the second video card and everything was finally there, but at 800×600. What a pain.