Interesting find on the primary node alignment. In terms of implementation - are you having, in effect, two complete copies of an entire sub in the .dat, one visible, one not, and one rotated vertically ?
If so ... not sure if this will cause CTD. If you've remapped all ID's, then it should. One thing I would recommend is removing nodes with duplicate names for;
rudder, torpedo doors, propellers, bow plans. These are refereced by name and not just ID in the subs .sim file - for example where a torpedo door name in the .dat does not match the names in the .sim, you get CTD. What I think you may have is one of the above items appearing twice causing a lookup failure / issue in the .sim file.
Whenever I work on torp doors, I always have the .sim file open at the same time and step through each tube in turn, if that makes sense.
Good luck.
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