NMD if its IDE or not, take the toshiba drive off and see if the stutter is there.
(assuming the toshiba is an IDE drive)
In a build almost as similar to yours,(apart from CPU) the machine would stutter during gameplay, bootup and the system would act up when listening to music/browsing the net.
I pinned it down to a glitchy IDE drive which after removal, was goodbye to stutter.
Mobo isn't that old w/ an ICH10R chip...but what of your PCI-E slots?
You can rule the GPU and slots out by putting it in the second PCI-E slot and see what happens.