Ok, finished and totally ported over. What worked was to copy the old configs over from BOTH the client and the server from 1.3.2 to the new 1.4.6 server. Tested the following method and vouch it works:
1. Install the new server, including mods. Run it once to build the structure.
2. Copy over the old config files for the server (and client too, assuming you have the mods installed for the new client)
3. Erase the world folder in the new server.
4. Copy over the old world folder.
Just have to make sure that you copy over the old blockID values in the config files, and then it works no issue.