So I tackle the project with gusto at this point, as a note, I think I switched mapping softwares at this point, since there is quite a bit of color difference all around. Though thanks to that I like to refer to the next phase of my project as "I go color crazy and change basically every color in the project".
As a bonus, this is why I didn't really use the in game map system, it sorta doesn't work well with pixels. :P