If your changing the "Mass" of the ship in the file below,
we are indeed talking about the same thing.
By changing the "Mass" or "Surfaced and/or Submerged Displacement" parameters of the above file the ship will sit at a different level. Throwing off the manual targeting ability of using the stadimeter to get an accurate range to target,
unless you correct the "Mast Height" figure in the .cfg file that I pointed out.
The height of the periscope makes no difference in manaul targeting, neither does the height of the sub. At periscope depth, or using the periscope fully extended while on the surface, makes no difference to the stadimeter reading. What makes a difference is the mast height figure in the Recognition Manual, and the true height of the target ship as it sits in the water.
As I said, using auto targeting will give you a correct firing solution. Manual targeting will be made unusable.
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However, I may be wrong. Are we talking about modding ships in general, or are you using the Fubuki through a self controled playable modification? If your changing the "Mass" or "Displacement" parameters to just make a playable ship work better this is quite different than changing a "target" ship for the sake of looks. I pointed out the problem thinking this was for changing a Fubuki used by the games AI. If your doing it to control a specific ship then I'm mistaken. I would suspect the last thing you would want is to have the thing shot out from under you.