what files are you using?
make sure you are using the Diplomacy converter to change the files properly
as for as the logisitcs/fleet crews just look
RESEARCHSUBJECT_MAXCAPITALSHIPS.....
RESEARCHSUBJECT_MAXSHIPSLOTS.......
as for cheating, well the AI uses the same research so its not cheating (though the game gets a little laggy with higher amounts of ships)
also Multi uses checksum numbers to make sure no one cheats and/or uses similar mods
We do it all the time with Distant Stars mod