I do not think the AI will make any changes, as it is incapable of designing any legal ship designs... it might add a research project if your queue runs out. If you have a CD-R drive you could burn all of the mods onto a CD and transfer them that way.
Here is the link to the patch in case it works:
http://www.spaceempires.net/home/mod...=getit&lid=341
Technically, you should be able to play your turn with just the data files (as they are all in the patch). You just won't see all the pretty pictures. Well... not sure what happens with missing planet images though. 8-O I know you can't get any detailed info on a component if the portrait image is missing. Probably the same with facilities.