The computer's primary user got impatient and asked me to do the reinstall. There were 3 files that weren't installed at the time, but I wrote them down. I initially had errors accessing things like internet explorer, but I was able to download SP3 through windows explorer. I put Malwarebyte's, Avast, TFC, and ERUNT and IE8 on a flash drive and installed them that way. I also had to reinstall my video driver but that was simple enough.
The repair install let me log back in and Malwarebyte's removed the spyware that prompted the problem in the first place. I'm working on an avast scan at the moment to find any more buggers and take care of them.
Had a few glitches along the way and have probably restarted the computer a hundred times today but my files I was missing from install are all in place after updating windows (Service Pack 1a, Service Pack 3, and 47 more updates later...) and at this point in time I've stopped receiving error messages so I guess we'll go from here ;)