This is a wonderful adventure reference map Jerett, really top-notch! I'm looking forward to the adventure when you finish it (I'm an avid Pathfinder player and DM, all of my maps are almost always geared towards our PF games).
I think the use of such mute tones works for this map piece, it conveys the feeling of a faded document. Along those lines the only suggestion I could possibly think of would be to blur up or feather the lines that still show minor pixelation (primarily just the outdoor roads/paths), and possibly even try to gritty-up the illustrated sections to go for an all-out document/parchment look. However, seeing as the image would be scaled down to page size, the rough pixel edges will probably disappear in the process.
Sooooo, awesome map!