Re: 'This save data was created with a newer version of the game.'
@SleepyCatTime Very strange that Origin didn't at least recognise the files already on your hard drive and decide to not redownload them all (you do have Origin set to look at, and install to, the correct drive? Have never tried running a game off an external hard drive so not sure if you have to do anything special to make that work).
If you're using mods, you shouldn't touch the package.mft number in the Patch folder, unless you have to temporarily remove the mod folder. Ideally the number in the merged mod folder package.mft should stay at 1 above the Patch one (which, if memory serves, is 12? So ideally your mod one will be 13). You should never need to set it as high as 99, if you're still getting the 'newer version of the game' message with the version number that high, something else is probably going on.
Looking at old threads of other people with this issue, some have said that completely uninstalling and reinstalling, or deleting everything but the contents of the 'Data' folder and reinstalling (should only be a small download if you do that), has fixed the issue for them. Probably the last thing you want to do, but hopefully worth a try?
Although I'm pretty sure you get a different message, it's also worth checking that you have all the same DLC installed (including the free multiplayer ones) as you had when you created the save games.