Just took the time to read through this whole thread... awesome job! I can't wait to see the finished version.
You probably don't need to rewrite much - code just becomes hard to read because there's so much of it, and unlike English text, it does not follow a quite linear pattern.
Just space it out and put comment headers for sectoins (about one header every half a screen is what I use, and then more for really confusing lines of code.
I'm not on my regular, DBpro computer reight now so I can't try it, but this could really make programs smaller - source code takes up much less space than EXEs do, and users could just download the EXE once, then download much smaller patches of the script code.
Great work!
-Xol