Implementation Guide Cleanup & deploy script url update

I think I accidentally merged in an unfinished change and so the "modified URL" defined in the create_projects function of the deploycoe script actually has no value and an error is thrown when trying to deploy via the script because the git remote isn't set properly.

Also, changed the layout of the implementation guide so you don't have to keep scrolling up and down different sections to navigate and added clarifying wording about which variables to specify as well as a short Troubleshooting section.