I'll take a stab.

The guide is pretty good. Follow it. The only unclear thing I can help you with (maybe). Is the stratum server you need to set up.  In linux U run it as follows:  

./mining_proxy.py -o stratum.mining.eligius.st -p 3334

notice the

-o  

and

-p

I am not sure if I am to have my local stratum server connecting to eligius using stratum? but it seems to be working well.

locally here on my net, the cubes are connecting to my stratum server using getwork. again , not sure if that is ideal. but it seems to work well for me.

....hopefully someone who knows what they are doing can chime in.