I didn't reinstall Windows but used Paragon Adaptive Restore which worked out surprisingly well.
Nevertheless I didn't get any benefit regarding pci performance, au contraire - I'm getting pci overflow on projects which worked before on the old mobo.
Several things come to my mind:
-pci sharing: maybe a case of Scope cards placement?

I'm still using a 2-slot passive Agp video card. Regretfully, due of its thickness I cannot place the two Scope pci cards close to each other. the agp is in between.

maybe I should buy a pci-e graphic card, so I could place the Scope card closer together?
-AHCI: at the moment I'm running in IDE mode, because of a Win XP installation. Would it be better to switch to AHCI ?
-unknown device in device manager on Pci 10 - I cannot figure out what this should be. Calls itself USB-Controller..
-I know Hyperthreading is recommended to be turned off. but here on the Asus B85plus there isn't such a feature (despite according to manual there should be this option). you just can turn off active processor cores (All, 1, 2, 3). but that's not what would help, or?