Redwine, I think you may be confused between port location and base location. They are different.
Your safest bet is to use the Mission Editor yourself and move things around.
To help you, let's look at some piccys of the ME. For this example, we want to move you three pens to the left at St Nazaire.
Figure 1 - current starting location.
Figure 2 - click on German base and move where you want to start.
Note the Lat/Long (m) figures in the status bar and apply to all files as previously mentioned.
IMPORTANT: The lat/long coords are linked to your mouse, not the selected unit. Therefore I would recommend that you save the LND file after making your change and then open the file in notepad, and copy the coords that were saved. Again, all it takes is one digit difference to break the whole thing.
Also, if you are fussy, expect some trial and error as you get the boat positioned exactly where you want it.