So I think I figured out what was causing the problem. When you invite someone or someone joins your game through steam invite, steam will restart your civ and kill the mod. This is why the other player will have "different versions of some game files". To fix this my buddy and I used...
SOS
Help. Having trouble with multiplayer. Every time my buddy joins the game it says "Player 2 has different versions of some game files. Verify that this is a trusted player" and then places a "*MOD*" before his username. When we start the game it says that our game is out of sync.
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