If you're able to access and work on your listings here, I don't see why you wouldn't go ahead and list them. I wouldn't list 1 or 3 day auctions but 7 or 10 day listings should be fine. In other words, Google is going to update their scan eventually, and probably sooner than later.
Once again, the malware is gone. Any warnings you or your customers are getting are false alarms caused by Google's lag in updating its information. Nobody's getting infected from your listings.