After trying some more and a few days AFK I finally managed to get Noggit working, but another problem comes up. When I have made a new continent as explained in Eluos guide and put the ADT, WDT and DBC files in my WoW folder to load in in Noggit the custom continent does not show up in Noggit.
At this point noggit won't show up your new instance because you will have to put the Files also in the wow folder and not in the patch beacuse noggit sets the priority of the dbc files to those who are extraced into your wow folder.
So just take the dbc,the adts and the wdt files and put them in to the wow folder like this:
For adts:
wowfolderworldmapsyourawsomeinstancename
For the dbc:
wowfolderDBFilesclient
This is where I get stuck. I have created the folder treepath for the ADTs and the WDT and copied the folder which contains the edited DBC (when extracted with Ladik's MPQ Editor the folder is also called DBFilesclient) to the root of the WoW installation path, so that it looks like E:/Program Files/3.3.5 Private Server/DBFilesclient and E:/Program Files/3.3.5 Private Server/world/maps. Doing this still does not make the map show up in Noggit. If someone can help with this problem that would be really appreciated.
~oekel