Look at this in reverse. In your Applications there was a main folder for the Ap, with 4 items. Deleting these and (ultimately)replacing them does no good at deleting the prefs files. [BTW,on it's way to the trash, "copying" ought to build this script, but it doesn't.]

"Users" contains Preferences, which contains the LimeWire folder in question. LAST, {as a matter of pure determination,} you threw out the INCOMPLETE file. This my friend is all I can see to do. The only other files that it uses, and marks as recently changed, are JAVA-type stuff and Apple kernels.

Not that this applies to you, but one time I put the System disk [10.3.9] in my drive as if I were attempting to (cringe) re-install, and it fixed a similar problem when I booted-up, although I had done nothing with the disk at all.