The problem is I've always operated under the assumption that the web comic was a living breathing thing until it went to print, at which time the printed sections would be canon. The prologue, the only complete singular portion of the story just isn't ready for canon. But I need books to sell.
The solution: proto-canon. I will print an extremely limited edition of the prologue as is (almost as is, color correction, re-lettering a lot of it, etc.). While I'm in the middle of this process I'm changing from a page format on the web-site to a "web toon" format. I'll explain more about this when I have time. But here's a comparison of the old page format compared to the new website format. In the end the printed version will be a different visual experience than what people get from the web.