Here are a couple of the links that I used when first getting into Squid. We run it on many Windows machines.
I remember one of the hardest challenges (for me anyway) was installing Squid as a service and then hiding the output. I will continue to look through my notes, but here are a few of the my Squid bookmarks:
This one has some commnad line switches:link and this one is more of a guide guide
I will update this answer with better info when I get to my office this morning and can look at my notes.
EDIT: The command that I am referring to that will run Squid as a service (at startup) and hide the output/command window is squid -i -n squid -O "-D"
Also, in my setup, the Squid folder lives in the root of the C drive. For configuring the .conf file I referred to a bunch of different Linux sites.
ANOTHER EDIT: Because I am an idiot, I actually just now read your entire post and have downloaded the .zip. My apologies for not posting any useful information and thank you for the zip (which I will comment on once examine it).