I agree that conditions during the shipment and storage on either end will probably result in a poor fit, even if you can match up screw holes or dowels. The dowels would help a great deal, but would constitute at best a fair guarantee.
The floor where you assemble the layout anew will not be the same as the floor on which it was initiatlly assembled, and even walls are often not square or vertical.
So, what you must do is to assemble them roughly but with the rails aligned as you need them to be across the gaps. Clamp...hard. Re-drill and drive in new wood screws or bolts. Shim under legs that are left slightly suspended. Once you have the modules screwed together with the only goal of an initial proper rail alignment between modules, it really doesn't matter too much what it looks like on either side. You can modify the terrain and hide any unsightly breaks in the terrain.