Why did you separate the SQM file to convert it?I had some trouble today with a MP mission, which I finally solved by loading it into the 2D editor, changed a unit to "player" and saved it. Then loaded it into 3D editor, and it converted mostly fine. Still had to do a *lot* of fixing to do, mostly on synchornize changes and waypoints.
But your problem is when loading the mission, right? My guess is that you are missing a script or something you referenced outside the mission.sqm file. Best advice is to do backups and try to isolate the problem by deleting stuff.
Good luck!