Yes, work to seal around the jack, as well as the wire exit points where they head out from the cups and to the headband to reach the other cup. You don't want a leak in that area either. I've tried to use hot glue for this activity before, and it is just plain horrible to try and end up getting a good job when applying. The hot glue globs a bit and ends up cooling off too quick. Then, with time (cable twists, etc.) the hot glue can tend to work its way loose. The silicon is a great option to consider. I found some smaller tubes of it at Walmart and they have a top on the container that you can use to re-seal the tube if you need to use some more down the road. It's a bit under $4.00 and much better than a regular tube that would essentially go to waste because if you don't use all of it, sealing off the tip is a bit of a pain so air doesn't reach it.
As to the imbalance, I've never narrowed it down to the plasticine amounts in the cups. That has never been a variation for me. The best way to resolve this is with Deoxit - with a quick spray into the jack on the ear cup. Then, use the V-Moda cable as suggested above. These two methods for a resolution have been mentioned more than once in the thread, and I've been following it strictly, and haven't experienced any additional imbalance issues with mine.
Best of luck!