Good grief, I feel like this map is a comedy of errors. So, I finally get everything broken up, cgpsmapper churns out the image files, and mapsettoolkit does it's thing and installs them in mapsource. I'm felling good, and then I start to notice that some little tributaries here and there are missing on the map. I noticed because I was checking areas that I frequent and have USGS maps of. So I go back and load it all up in global mapper and it looks fine. I check cgpsmapper error logs, and it had a bunch of "Not enough node" errors. After some searching and testing I think that the problem is how I broke up the flowline data. That even though it is all displaying correctly in Global Mapper, that the polygons aren't quite right. So, I've gone back to the flowline data to try and re-process it. Very aggravating.
My home internet connection has been having some issues, so if I go offline for a few days don't worry. Hopefully I'll finish with the processing by then. Luckily I kept all of the raw downloaded data so I don't have to download it again. It is grustrating having everything right except the flowlines. Bah. Good luck on all of your map efforts.