Can you show us a picture of the underside of the roof or where the joins would be? There may not be enough room to drill through to place magnets, but you might be able to glue them to the walls where the corners meet, etc. You could use magnets as stoppers as mentioned by Diddick above. I've done a bit of work with magnets for another game system where a base model could have different weapons, and as long as the piece is a couple of mm wider than the magnet you can make it fit (make sure you test the poles before you glue the second side).
btw, I never commented on the paint job, I really like it