Don't quite get what you are saying.
No you didn't always have the virus I did not say that. And yes it is a good Idea to uninstall your AV some viruses have the capability to disable the ability for certain AV to find them once you have opened the file and become infected.
There is no reason to uninstall LimeWire it is not infected. The infected file / files may be in the share or incoming folders but uninstalling LimeWire does not remove those files / folders.
If a person is still getting new multiple copies of files the same size without downloading them then they are still infected.