its ironic the time when i'm presented with a good amount of free that the game that i want to mod is near death along with its community it seems.

anyway, how does someone mod cortex command and update mods that are out of date like this http://forums.datarealms.com/viewtopic.php?f=61&t=21377

If there have been any changes to the places resources are located (if you used some resources in the base game distribution, for instance) you'd have to go through and change all the old references to the new ones.
I don't think Lua has dropped any functions, but things might have changed a bit so you may need to check that as well.