So I went through and focused on simply reorganizing things. No major code changes, just cut/paste into a new solution. The thing at least looks vaguely professional at first glance now. The solution is up to 7700 lines in 120 code files, nicely organized into a sane directory structure.
The next step is renaming some of the things that are not-consistent across the project. After that will be additional comments and actual logical re-arrangement.