Install for Dummies

Following your guide I was able to get GitLab-Pages up, however everything except the index throws a 404.
What works
Login
Enable Project

What doesn't work
/webhooks dir throws a 404
/pages dir throws a 404

I am sure I am just doing something wrong.

So when you enable a project, it does yet automatically pull the latest code. There is an issue for that #17.
So it may be that you need to push to your deploy branch and that should build the project page.
Let me know if that works or does not.

That was where I started. I got the webhook working. This does not like to be proxied, it will not work.
I pushed a change, and saw the webhook be called.. however

That does not work. I even put a index.html manually in the publicdir folder.... still get 404?

Could you take a look in the project's .tmp/ and pages/ directories? The .tmp is where clones go, and pages is where the final Jekyll static-content website goes.

I'd recommend taking a quick read through #15 (comment)
Another user found that one of the checks to see if a project is enabled would sometimes fail. That if statement would cause problems for their setup and found removing it was their workaround. See #15 (comment)

I currently do not have much in the way of debugging tools for GitLab Pages. I would highly recommend simply adding debug statements throughout https://github.com/Glavin001/GitLab-Pages/blob/master/routes/webhooks.js#L14 until you find where it stops executing and fails and then let me know where.