First off, others have talked about how commentors are a small percentage of readers, so really the best way to get more comments is to increase overall readership.
One thing I have seen on someone's weblit site was a comment prompt at the bottom of the chapter (clearly separate and subordinate to the story text above). It was usually in the form a question or two related to the current chapter that people could respond to in a commenting section immediately below. If you wanted to drive a community on a separate LJ group account, you might try linking the prompt directly to that community where people could respond, if you decided to go that route.
Is it going to hurt you in any way to setup the lj community now? If not, then I don't see why you can't go ahead and do so.
As for alternatives, well, you could always migrate to a different site that integrates story posting with a forum instead of maintaining to different locations. I'm thinking of the Drupal-built sites a number of weblit folks use.
I don't know which of those ideas would work best with your current situation, but those are a few things to think about.