After being frustradrs with the lack of info on conningtowers I went diging and found out how to change the conning tower.
*NOTE THIS IS FOR EARLT WAR TO MID WAR TOWER*
Go to My documents\SH4\data\cfg\SaveGames\ and wat ever carear you want to alter\ActiveUserPlayerUnits.
Scroll down to the bottom(about a little under a thumbs with on the scrool bar) and you should see this
Change it to this.
ID=GatoConningMedWar
NameDisplayable=The aft bridge deck fairwater was removed to reduce silhouette
UnitPartInterval=1942-06-01, 1944-12-01
Type=GatoConningTower
ExternalLinkName3D=data/objects/Conning_Gato_02
HullTextureNameOverride=data/Submarine/NSS_Gato/NSS_Gato_T01.tga
HullLightmapTextureNameOverride=data/Submarine/NSS_Gato/NSS_Gato_O01.tga
HullNormalmapTextureNameOverride=NULL
MenuSilhouetteTextureNameOverride=Gato_Class_02.tg a