We will have the Emperor discussion at later point. And I can recommend some books as well :)
Re the game: We can use the latest official set-up proposal or do standard alpha+3.
Last post in this thread is newest suggestion, but I am happy with standard: http://www.harrisgamedesign.com/phpBB3/viewtopic.php?f=40&t=7989&start=608
R/J: There is no penalty involved at all, other than Mongolians becoming pro Russian if J attacks a R territory neighbouring a Mongolian terr.
Science tokens: You buy a token for 5 IPC, a roll of 6 is a success. However, if you fail you keep the token and can roll next turn for it (and any new). Once you have a success, all tokens are discarded. You decide.
Bringing kid to bed now, might take some time :)