I also posted this in the Steam forums, hopefully this works for some of you.
While emailing saved games is OK, I found this troublesome and hit-or-miss as the desync can occur before the save and then you're screwed and have to start over. So, I decided to test using dropbox as a workaround with a friend. So far this has worked with no issues and is completely automated so there is no need to email or upload the save all the time.
The system I came up with is as follows, which works with a brand new game after turn 1 when a fresh save is made and not after:
1) Both parties will need a Dropbox account
2) Install Dropbox and create a save game folder to be shared.
3) Navigate to your saved game folder (normally found in "C:\users\<yourname>\appdata\roaming\the creative assembly\shogun2\save_games_multiplayer"
4) In the folder from step 3, move the file named "autosave.save_multiplayer" to your newly created Dropbox shared folder. In my case it was "C:\Dropbox\Shogun2"
5) Delete the file "autosave.save_multiplayer" from the folder identified in step 3.
6) Now using the command prompt you will need to set up a symbolic link in windows to allow the game to save correctly. The syntax for a symlink in this case is as follows, though you will need to change directory/username info specific to your system:
Effectively, this creates a shortcut to the file allowing you to change your autosave location.
7) The host will need to share the dropbox folder with whoever they need to.
8) Everything should be good to go.
Connecting Player Instructions:
The connecting player will need to do all the above steps except in step 4 instead of moving their autosave, they will need to take the autosave from the host's dropbox folder and place it in their dropbox folder which creates the initial saved game synchronization.
-It is strongly recommended you do not have any other save game data in your multi-player save folders
Let me know if this works for anyone. This has been working for my friend and me for about 50 turns so far with multiple loads (not continuous play).
Update: Completed a game with no problems using this and am now playing a RotS game with no problems so far.
Edit1: Changed formatting to remove ambiguity on connecting player's instructions