If you downloaded LW from Lime Wire » Download LimeWire then it's free of malware. The popups are more likely associated with the so-called 'accelerator' that you downloaded There's no link to any accelerator on the official LW site. There's more info about these dodgy things below.

accelaration patch
No more internet (not just LimeWire) thanks to Accelerator
2 easy questions for you smart folks
LimeWire Accelerator Patch?

If it was me, I'd remove the thing & scan for spyware & adware again. Also run an AV scan just in case. If you don't already have it, Ad-Aware is a good, free tool for finding adware.
Ad-Aware SE Personal (free)