BleepingComputer.com: efficient reinstall

Hi,
I installed Vista on my desktop a couple of months ago and did some very intensive work on the machine in the meanwhile (like e.g. putting on custom icons, adjusting Visata settings carefully, adjusting program settings carefully...). To my horror the installation was a failure. Just about every program crashes constantly and after trying everything I can think of for the last two weeks including but not exclusive to uninstalling and reinstalling many of the programs, updating all drivers etc...I have come to the conclusion that I have to reinstall the whole OS from scratch. I really dont want to lose all the work I put into adjusting the settings, changing the appearance of icons and other things. How can I keep all that good stuff and reinstall efficiently? I have a complete backup of the whole PC configuration on another hard disk. Any help would be appreciated.
Thanks,
Tod

I guess the obvious question would be, how do you know which is the good stuff, and which stuff caused the problems? I don't know the extent of what changes you made to the configuration, but the only real way I can see to fix it is to start over, and change things little by little.