Multiple DataBases really wouldn’t work with DM, because it’s main goal is to help with mapping relationships to objects. There isn’t much call for mapping relationships across multiple DBs.
Second, if I understand correctly, are you trying to merge multiple rows into one row?? That is an incredibly bad idea, as it makes the database really inefficient. There is no reason why your DB can’t handle hundreds-of-thousands of rows, unless it really sucks (like Access or something). Just set up proper indexing. If you know the database is read heavy, you can go nuts on the indexes to really help queries run faster.
Finally, DataMapper (original) doesn’t handle multiple relationships to the same object very well. My extension (DMZ, search this board) handles them better, but what you are doing doesn’t look much like a highly normalized DB. Unless your DB is normalized, I doubt DM will work for you, much less be very efficient.