Great job on scanning Next Generation magazines, marktrade. I'd easily recommend rescanning any issue you have.
As for me, I've only uploaded four Next Generation magazines: May, June, July and September of 1996. All of the rest are from someone else, so those comparison pictures you're showing aren't from my scan. The issues I scanned were to fill in holes of digital collections I've come across, and they're all posted in my upload thread (I haven't done anything in a good while, due to other projects). I had plans of going back and redoing some of the posted NextGen mags, because their quality is generally poor/average, but when you're using a flatbed scanner those large Next Generation magazines are very daunting.
Also, I wasn't aware of using a heatgun to separate pages (I actually have a heatgun I could use, oddly enough). I use an exacto knife and try to cut as near as I can to the edge of the page. I've noticed my uploads are better than most for preserving edges in comparison, but your method has really produced the best two-page spreads. Is there any trick to using the heatgun? You just point it at the bind until you can tear the pages away?
As far as color and editing on my issues, I use the standard setting from the scanner, then snip the ends of the level chart to make the blacks and whites closer to black and white. Color is a tricky issue, and I generally don't mess with it. I find the blacks and whites more important since it makes text easier to read.