Hey there - sounds fantastic.
I'm doing quite a similar trip - 3 months will be fine :-)
Take a look at the route we've planned to take in September
Route » Journey To Russia (scroll down for the map)
We've shifted it slightly now so the run back home takes in a little more of Austria, but it's broadly correct.
We've decided to stay in St Petersburg for a couple of nights rather than Moscow - everyone we talk to says the same thing - Moscow is wonderful to visit, but not to spend any time there.
The plan is to hit SP about lunchtime the first day then spend the rest of that day and a 'rest day' there - then carry on down to Moscow - spend the night about 70 miles outside the centre, ride in first thing in the morning, do Red Square etc, then in the late evening ride about 70 miles back out to camp.
There's a whole wealth of information you'll find useful on HUBB - use the search tool which really is quite accurate:
http://www.horizonsunlimited.com/hubb/search.php
Or for more simple boiled down information, you could try our country information pages, which really are just notes for us, but you may find something useful in there.... you'll be the first... but you never know!
Country Information » Journey To Russia
Good luck and enjoy the trip - I'm sure it'll be a blast.