In your runLime.sh you will find a line lik this:

CLASSPATH=".:collections.jar:xerces.jar:MRJToolkit Stubs.jar"

change it to something like:

CLASSPATH=".:/path/to/LimeWire/collections.jar:/path/to/LimeWire/xerces.jar:/path/to/LimeWire/MRJToolkitStubs.jar"