You need clean areaids and created maps for server. This need a fixed extractor.
Maybe this helps you viewtopic.php?f=10&t=7382
I think I still have extractors that read custom mpq called 'Patch-M' somewhere but I think it would be more useful teach you how to do for your customs mpq.I hope you use custom build of TrinityCore otherwhise I can't help you.
https://github.com/TrinityCore/TrinityCore/blob/master/src/tools/map_extractor/System.cpp#L94
Did you save your work once with noggit 1.3?Earlyer versions dont generate the needed data right. Backupnyour files before!