As most of you know, Van and I had our own personal challenge so I'll repost mine here:
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While not as bad as Obsydian Shade's I think you're going to have many of the same problems.
Most acutely, because of the big sonar the TT room will stretch so far back that you'll have torpedoes in your command room.
Additionally they're so low that they're likely to interfere with the battery installation.
Thanks for the input Thiel, I didnt consider that, as for how low the tubes are, the US SSKs have them about at that height, but I will double check.