Run msconfig (if its still around in Vista) from "run apps" and take a look at what loads during boot. If you find entries with the names of the modules, delete them. The error messages may be a result of malware-affected config files trying to load the removed malware, and since they have be removed, you get an error saying that the files cannot be found.

It is a good idea to do another check to see if you have the malware 100% removed as GecT suggested.