A.Have you got external harddrives? if so remove
B. Change PCI slot, the nearer the chipset the better
C. Remove all background processes
D. Ramp up buffer settings
E. Defragging at this stage shouldnt affect anything
F. update USB drivers
G. Update graphics drivers
H. check in managment for drivers that display the ! icon

I know i've gone over solutions others have mentioned, im just brainstorming here... to my mind the solution is gonna be a simple thing, something you overlooked, the crackling is obviously system wide and therefore is system related rather than a specific software problem. stuttering in my experience at system level is often related to a component or driver problem.

if i think of anything else random ill post... in the meantime im feeling ya pain, its so frustrating...