I don´t remember all steps, but there are few things to consider. The MPP Import packages contain a few folders named "Fixes". One of these fodlers contains a Part.xml. This one overwrites your defaut Part classification.
What you have to do is to merge (!) your classification with the MPP classification. MPP needs the Phantom and the MBOM category.
1. First you have to get your own Part classification via AML or SQL. You need the text that is used in the class_structure property in your ItemType.
2. When you use a multi-level classifcation, try to understand how the property works. It´s an xml like structure. If you corrupt the structure, you will get into trouble.
3. Merge the missing MPP classifications to your own class_structure string. I am not sure, if you can use the new classes as Sub-level classes. I used them at top level, just like it´s done in the default configuraiton.
4. Edit the Part.xml to use the new classification string
Try this one in a testdatabase first! I do not guarantee that this information is correct.
We use 11.0SP11, publishing service works fine. I remember that there are certain codetree files that contain information about which version shall apply. E.g. ConversionServer -> web.config -> scroll to bottom -> bindingRedirect property indicates version
But I would recommend asking the support to help you there. I would not recommend to change these files by yourself. I am not sure, which additional codetree files are related to this values.