The latter problem is slightly easier to "solve" so I'll address it first. A common confusion the non-techy types seem to have is with Java/Javascript. They are both very different languages when it comes to the way they are handled, so Flash/Java Plugins have absolutely no bearing on Javascript errors.
However, you don't say exactly what you're errors are, and you have done very little in the way of diagnostics for us - probably because of the confusion outlined above. Is it only on specific sites you get the errors, and if so can we have an example of one that doesn't work? Or is is with every page you visit?
For your Yahoo! messenger program, you also seem to be barking up the wrong tree; IE and Firefox again have nothing to do with Yahoo! messenger, save for the odd additions of shortcuts in the menus.
I suspect what has happened is that you may have inadvertently deleted or have corrupted a file it needs to operate. Generally, reinstalling the app would replace all the files with nice new clean and working ones. Try it, and if it doesn't work, do come back.
