I believe that opening the old VI's and re-saving them in LV 4 would also work. If you don't have LV4 or 5 then a conversion kit for old VI's is supposedly available from NI.
You might be able to find a workaround for problem (2) by temporarily moving some of the problem VI's out of where they currently are in the hierarchy (vi.lib?) before you load your old VI's, and/or creating 'wrapper' VI's to go around the new VXI VI's that have the connectors in the places you need. If the conversion in (3) is a problem, can you avoid it by saving the VI's into an LLB on the Mac before bringing them to Windows?