There are various options. I have done it numerous times. From the description of your problem though, it sounds like you need a clean install. (I think I may be doing the same thing on my father-in-laws machine tonight due to problems with IE.) You really don't need to redo your hard drive, but you do need to get rid of everything related to the windows installation. The easiest way, as a previous post suggested, is to delete the windows directory. If there is anything in there you need, obviously save it beforehand. Like mail files or favorites which you can restore into your new installation after. "DELTREE WINDOWS" should do it. It will take a while and you need to boot to safe mode command prompt only to do this using the F8 key. Then you can boot your system from the CD and do a new install. Make sure it goes into the C:\Windows directory when you get to that point in the install process. When you are done, you will have a bunch of old programs left on your machine which are basically useless. You can weed and prune them out, which is probably the best option, or install another install on top of the left over installation. But it isn't a real huge deal and does give a very nice performing machine afterward. Once you are done, if you have a nice high speed internet connection, bring all of your hardware drivers up to the latest and then go to Microsofts update site and bring windows up to date. Have fun, you do have a bit or work ahead of you.
A note of caution: Do not leave any of the old windows on the machine, a new install over an existing windows or even on a machine with windows in a renamed directory usually carries over the registry with it and the source of your problems is probably in the registry. You need to make sure all remnants of the registry are gone.