I had to do this process twice, and here's what I've learned:
1) The motherboard does not need to be removed. I suspect this guide has you remove it so you don't damage any components when heating the screen, but there's no physical reason to remove it.
2) Yes, passing the digitizer cable/chip through the hole in the plastic housing is a royal PIA. I may have ruined the first screen I tried it with. Doh! For the second go round, instead of removing the LCD (like Hector recommends above), I just made the hole bigger. How, you ask? I took an emory nail file and trimmed it with scissors to be just narrower than the hole - then I filed away! With a few minutes of careful filing, I was able to double the size of the hole the cable has to pass through. Voila! There's still plenty of plastic left for the double-sided tape to be applied on the inside. Just be sure to clean up all the plastic dust first with a small vacuum or Q-tip before re-installing the screen.