Kriller you mentioned in your read me,
"if you think the sub is sitting up too high then use the dive rate mod it will lower the sub but reduce roll pitch effects"
...now i have seen your stock setting with PE3 and I did change to the dive rate option... BUT, fact is i think you nailed it with where you 'placed' the sub int he water.
it looks high when viewing externally but when you look at this picture of the USS Pampanito youve nailed it. Look carefully at the distance between the bottom of the dive planes and the water line, as well as amount of freeboard showing on the side of the hull.
in fact i think i may have just talked myself into switching back to your PE3 without dive rate option....
your setting may look unnatural to some initially but by looking at these photos it seems spot on realistic....