well another valuable lesson from the dog's seemingly never ending results of additions:

I now run 3 variants of CFS3....
1) Stock ( well with the usual scenery, gunsight, missions, effects ,ships... ect... )

2) Battle of Britain ( with all the same addons as above )
to do this install, simply "copy " the stock game and rename it, then direct the install to that folder during the install.***

3) Korea ( it makes it's own game by copying from the stock game the files it needs , and even makes a separate set of Documents & Settings files*** )

*** the reason I show that ***

when you do multiple installs of CFS3 , you must make a set of default doc's n settings files for each install, or it will corrupt your game versions. ( learned the hard way )
Korea did it's own , but read further...

But once they did that.... to defeat the error,
I changed the files mentioned ( in  the C: Documents and Settings / Main Named User / Application Data / Microsoft / Combat Flight Simulator 3.0 )
  to BoB3 ( for that install )
then simply deleted the CFS3 stock folder from the main Microsoft game folder , and reinstalled for my stock game.
Now 3 fully multiplayer enabled installs now, no cross referencing, or errors. But alot of hard drive eaten up.

The Historic missions in the battle of britain install are awesome to fly. the korea game gives a new set of flight rules to adjust to ( the Mig 15's are tough to beat in a turn )
and then the stock game isnt bothered by strange errors of scenery or mission errors.
hope this helps someone who considers this in the future.

Cheers !  and  good hunting !

As Mathias stated, Martin Wright's utility is the perfect ool for this. Anyone that has installed Korea has seen the results of this utility as it is what our installer uses to create the stadalone copy.