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Well the modifying of the templates really doesn't seem to be the problem. It still generates a new topic for each comment unless someone specifically clicks on "reply" to a users specific comment at least from what I could tell after looking at the specific forum after doing the import of a module.
I didn't try to create a new comment to see how it would list them. Maybe the problem is in the importing, perhaps if the first comment to an item was used through the d3forum comment integration all of the comments on that item would stay under one topic. I will experiment with this and report what I find.