I did not even read your post until I was 3/4th way of completing the project, which took something like 15 hours. Hah. Thats incredible. I'm looking into your reputation point problem now. If others are experiencing problems, it may be time to recalculate all reputation points, which is never a good thing as someone is sure to get very upset when they lose points.
I checked it out. Either a whole bunch of people dropped an atomic bomb on you by rating your posts down, or there is a kink in the system. There was no alteration of your actual account: It had to either be a miscalculation of points due to the upgrade or people really did use their reputation power to knock you down to -200. Wow. I don't know that others are having this issue, but I am going to put you back into a positive range.
As far as the site, how do you like the new design? This new version of the forum software is in the final release candidate stage and will go gold in several days. The site tends to have a different look between IE8 and Firefox. This is interesting, because although Firefox will not render some transparent images, it will do curving on the tables that IE is not capable of performing. I encountered this many years ago. Firefox says, "I can't redesign an image so I won't even render it, and I'll curve the thing instead" and IE decides to just show you the image.