This is probably just a shot in the dark but you might want to try and uninstall LimeWire and Java again. Then go in and find your .limewire folder and delete it again. After you complete this download Java the offline installer and LimeWire from the official site. Install Java first then install LimeWire. This sounds like a Java issue you should only be using 1 to 3% of your CPU with LimeWire.
http://www.java.com/en/download/manual.jsp http://www.limewire.com/english/content/download.shtml