A Kyrgyzstan visa is very straight forward and simple to get in Tokyo.
Cost for Americans: ¥8000 JPY for a 30 day single entry tourist visa, payable by wire transfer (ATM) with receipt due at pickup time. NOTE: The consul will tell you that you don’t need a Kyrgyz visa if you have a multi-entry Kazak visa. Getting a M-E Kazak visa is a bit of a pain and as this is a new policy as of July 2012 (which means that border enforcement might be iffy), we just got a straight visa from Kyrgyzstan (costs more, but potentially less hassle).
Website: Kyrgyz Embassy of Tokyo