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good question; the only way i've been able to generate valid json to load into mobile content server is to create web map on arcgis online, then view the json of the web map. I copy/paste the json structure into the mobile content server, which can then be browsed to on iPad.
The way I understand is that all layers you put into arcgis online have to be in WGS84, so I assume the same holds true for the mobile content server, but I could be wrong. Mobile content server capabilities are limited to what can be achieved in arcgis online given my workflow. I havn't been able to find documentation on how to hand-craft valid json for the mobile content server, outside of using arcgis online.
IMO, the mobile content server in server v10 is under developed, and hard to find info about. I'd look forward to future development in 10.1 on this portion of server.