Thats exactly what I do.
For example I choose the custom map "bloody_gulch", unpack the server.zip and client.zip and delete them. Now all the unpacked stuff lies in front of me. I update the init.con and replace old classnames by new ones, here taken from "st_lo_breakthrough/server.zip/init.con".
Next I move all the map packing scripts to mods/fh2 and run "pack-map.py".
cmd opens up and asks me the maps name. I type bloody_gulch and hit enter.
After a short while its done and there are new server.zip and client.zip files.
I run fh2, launch the map in coop, it is loading, I hit join the game and voila - there are still no soldier classes to choose from. I try to spawn and the game crashes.
What did I do wrong?