First of all, I don't understand why the speakers are not lined with anything. While the enclosure is inert and shouldn't have any standing waves, there's still going to be some interaction inside due to the small rear port hole, there's no way around it. Secondly, the crossover is directly behind the woofer, inches away, 'nuff said. How about mounting it on top behind the tweeter? Anyway this is what I did:
I lined the inside of the 6.9SM with lambswool and cover the crossover with the lambswool. I just can't believe the improvement that it has made to the sound. I thought that it might diminish the bass output, it hasn't. The bass is now tighten and very define and coherent. The sound is more distinct and focus. I could go on and on using all the audiophile adjectives, bottom line is try it yourself. It is very cheap and easy to do.
The next weakness that needs to be address is the baffle is not as inert as it could be. Touch the area between the tweeter and the woofer while playing some loud music and you'll know what I mean. Would gluing more wood behind the baffle take care of that? Don't know, we'll see when I have time.