Howdy spectratone,
You need to rejet your Mikunis. There is little to be gained by changing the thermostat or fan or anything except the jets. You could build a stove box around your header and use it to warm the intake air, but beyond that there is little that can be changed external to the carbs.
I am pretty sure several snowmobile manufacturers used Mikuni carbs, so it is not a hopeless task, only one you will need to learn how to do and then do it at least twice a year; maybe more often if you live in an area with a wide temperature swing.
http://www.jetsrus.com/main_page.htm
--
Mr. Shannon DeWolfe -- (I've taken to using Mr. because my name tends to mislead folks on the WWW. I am a 51 year old fat man ;-) -- KD5QBL
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