Seth,
I didn’t read the entire thread so someone else may have given you good info already, but here is what I would recommend.
First download and run AdAware. This is a great freeware program to eliminate spyware. When you run it check all the boxes and have them removed. If you us any sharing software like kaazaa it will cause those to stop working, but you can reinstall.
As for things running you didn’t want to at startup you can run msconfig by going to start/run and typing msconfig. It has a startup tab and you can eliminate unwanted items here.
Lastly make sure your hard drive has at least 100 megs available and do a scan disk and defrag.
If all of this would fail I personally would start thinking reformat.
Good luck