Even after malware has been removed from a computer many of the problems caused by it may still remain. That said, one of the first things you should do in order to fix any of these problems is to make sure that all infections have actually been removed. If you know that you still have infections on your computer then, instead of trying to fix problems while the malware is still present, you should first remove all infections. To do this please see my article about How to Clean An Infected Computer. Then, after you believe that all malware has been removed you should also check to make sure the computer is now clean by following the advice I give in How to Know If Your Computer Is Infected. Trying to fix problems on a computer that is still infected is largely a waste of time.
Once you have confirmed that your computer is entirely free of malware you should then back up all of your important files. This way if anything goes wrong while fixing the computer, which is a very real possibility, your important documents will still be intact. Please note that if your computer cannot boot you should follow the advice on this page in order to back up all important files.
In order to fix your computer you only need to follow this article as far as is required to fix the problems you are experiencing. However, advice on how to fix nearly any type of problem is included in the article. Thus, the length of the article is actually much longer than just about anyone would have to read. Just consult the sections that are relevant to the problems you are experiencing. Note that for situations in which your computer will not even boot into Windows you should skip to the section about What To Do If Your Computer Cannot Start.