Well, Actually it is quite easy, first of all you need to rename your bridge set folder to name you want, then you move to SCRIPTS, there are two folders with files you'll need to edit 1: BRIDGE, 2: CUSTOM->AUTOLOAD. In both of these folders there are plugins you need to edit and rename.
I'll take for example PDW Excelsior bridge plugins, lines that are marked with red color are those you need to rename with the same name of the folder where bridge model and textures are as well as the plugins names.
this is the plugin from SCRIPTS/CUSTOM/AUTOLOAD directory (this file stores informations about animations used on specific bridge as well as map swapping, active LCARS and sound functions) : 
import Foundation
# Uncomment the below to enable!
Foundation.BridgeDef('
PDW Excelsior', '
PDWExcelsiorBridge', dict = {
   'modes': [ Foundation.MutatorDef.Stock ],
   'locations': {
      'AmbHelm':   [ 'data/animations/Amb_stand_h_m.nif', 'Amb_stand_h_m' ],
      'AmbTactical':   [ 'data/animations/Amb_stand_t_l.nif', 'Amb_stand_t_l' ],
      'AmbCommander':   [ 'data/animations/AmbTNG_seated_C_M.nif', 'AmbTNG_seated_c_m' ],
      'AmbScience':   [ 'data/animations/Amb_stand_S_S.nif', 'Amb_stand_s_s' ],
      'AmbEngineer':   [ 'data/animations/Amb_stand_e_s.nif', 'Amb_stand_e_s' ],
      'AmbGuest':   [ 'data/animations/Amb_stand_X_m.nif', 'Amb_stand_X_m' ],
      'AmbL1S':   [ 'data/animations/Amb_L1toG3_S.nif', 'Amb_L1toG3_s', 'pCharacter.SetHidden(1)' ],
      'AmbL1M':   [ 'data/animations/Amb_L1toG3_M.nif', 'Amb_L1toG3_M', 'pCharacter.SetHidden(1)' ],
      'AmbL1L':   [ 'data/animations/Amb_L1toG3_L.nif', 'Amb_L1toG3_L', 'pCharacter.SetHidden(1)' ],
      'AmbL2M':   [ 'data/animations/Amb_L2toG2_M.nif', 'Amb_L2toG2_M', 'pCharacter.SetHidden(1)' ],
      'AmbG1M':   [ 'data/animations/Amb_G1toL2_M.nif', 'Amb_G1toL2_M' ],
      'AmbG2M':   [ 'data/animations/Amb_G2toL2_M.nif', 'Amb_G2toL2_M' ],
      'AmbG3M':   [ 'data/animations/Amb_G3toL1_M.nif', 'Amb_G3toL1_M' ],
        },
   'CurrentMaps': {'Map 4': "Map 4"},
   'GreenMaps':{'Map 4': 'data/Models/Sets/
PDWExcelsiorBridge/High/Map 4.tga'},
   'YellowMaps':{'Map 4': 'data/Models/Sets/
PDWExcelsiorBridge/High/Map 4.tga'},
   'RedMaps':{'Map 4': 'data/Models/Sets/
PDWExcelsiorBridge/High/Map 4_r.tga'},
      },   
} )
in the very same file you'll find these lines :
"bridgeSound": {
         "LiftDoor": {"volume": 1.0,"file": "sfx/
PDWExcelsiorBridge/ebdoor.wav", "group": "BridgeGeneric"},
         "AmbBridge": {"volume": 0.3,"file": "sfx/
PDWExcelsiorBridge/ebamb.wav", "group": "BridgeGeneric"},
         "RedAlertSound": {"volume": 1.0,"file": "sfx/
PDWExcelsiorBridge/RedAlert.wav", "group": "BridgeGeneric"},
         "YellowAlertSound": {"volume": 1.0,"file": "sfx/
PDWExcelsiorBridge/ebYellow.wav", "group": "BridgeGeneric"},
         "GreenAlertSound": {"volume": 1.0,"file": "sfx/
PDWExcelsiorBridge/ebGreen.wav", "group": "BridgeGeneric"},
         "ViewOn": {"volume": 1.0,"file": "sfx/
PDWExcelsiorBridge/ebviewscreenon.wav", "group": "BridgeGeneric"},
         "ViewOff": {"volume": 1.0,"file": "sfx/
PDWExcelsiorBridge/ebviewscreenoff.wav", "group": "BridgeGeneric"}},
   "LoadingScreen": "data/Icons/LoadingScreens/
PDWELoading.tga",
bridge sounds using BP Core (Bridge Plugin Core Gold to bo specific, which comes with KM 1.0 mod) can be placed into folder you'll create and name after your custom bridge in SFX sound folder, on the bottom there is custom loading screen for your bridge. Once again I marked lines you must alter in order to get it working properly. 
Whole point is to find anything related to bridge name in this case it's PDWExcelsior
Same thing with bridge plugin file stored in SCRIPTS/BRIDGE folder, you need to rename all lines with name given to your new bridge, mainly these are just directories to your bridge set folder, you should be only interested in these lines at the very beginning of the file :
def CreateBridgeModel(pBridgeSet):
   iDetail = App.g_kImageManager.GetImageDetail()
   pcDetail = [ "Low/", "Medium/", "High/" ]
   pcEnvPath = "data/Models/Sets/
PDWExcelsiorbridge/" + pcDetail[iDetail]
   # Pre-load the Bridge model and viewscreen
   App.g_kModelManager.LoadModel("data/Models/Sets/
PDWExcelsiorbridge/Yamaguchi.NIF", None, pcEnvPath)
   App.g_kModelManager.LoadModel("data/Models/Sets/
PDWExcelsiorbridge/YamaguchiViewScreen.NIF", None, pcEnvPath)
   # Load the viewscreen and set it up specially with SetViewScreen()
   pViewScreen = App.ViewScreenObject_Create("data/Models/Sets/
PDWExcelsiorbridge/YamaguchiViewScreen.NIF")
   pBridgeSet.SetViewScreen(pViewScreen, "viewscreen")
   # Setup bridge object
   pBridgeObject = App.BridgeObjectClass_Create("data/Models/Sets/
PDWExcelsiorbridge/Yamaguchi.NIF")
   pBridgeSet.AddObjectToSet(pBridgeObject, "bridge")
   pBridgeObject.SetTranslateXYZ(0.000000, 0.000000, 0.000000)
   pBridgeObject.SetAngleAxisRotation(0.000000, 1.000000, 0.000000, 0.000000)
that's about all 

so to sum it up, it's all about renaming bridge name lines with your custom name and be sure they are the same everywhere otherwise there will be a BSOD caused by faulty name/typo insidfe the plugin ;)