I suppose the iia and the iiia are the same from this popint of view. When i re-assembled my iiia, the only way to put the lens mount back was to put it back in the same time with the rangefinder unit (i mean the little wheel-thingies and the rotating small lens behind the wheel, NOT the long prism which i did NOT remove). The alignment of the whole thing is based on the connection between a cog wheel and the "cogged" region of the lens mount, through a hole cut in the outer shell of the mount. I'm talking about the lens mount in the camera body, of course, not the lens itself.
When you put back the lens mount into the body shell AND the rangefinder unit, you can align the rangefinder unit as you want and fit the things back. When i did this with mine, i discovered that there were two scratches made on the two rotating cog wheels of the rf unit. When those two scratches are aligned, the whole rf unit was well-aligned for infinity.
If this does not help, i'll try again saying it in a different way - however, check also Henry Scherer's pages where he shows a disassembled contax iiia rf module.