That is truly a beautiful and impressive demonstration of code analysis and reduction. It reminds me of a very similar exercise I had to do in C about 15 years ago, taking someone else's War and Peace-sized copy/paste extravaganza and boiling it down by creating subroutines with appropriate parameters (so it could compile and run on MS-DOS, 15 years ago). I was appalled that the author of the original monster had presumably majored in Computer Science. I was only several weeks into learning C at the time, but had already spent a few years with FORTRAN, so successful code analysis was very much a matter of having practical experience.

Alas, in the current situation, the sad thing about NMRsucks's first opus -- whether reduced or not -- is the complete absence of a sensible algorithm, and the apparent lack of an appropriate spec for what the process is supposed to do.

Your repair work is inspiring and instructive, and I applaud (and ++) that, but the program itself is still basically unworkable, and the OP will be better off starting over from scratch, after he figures out how to explain the goal properly.