first let me say that it is possible to use the train with the bike.
I myself have so far used it only over the border in and out of Mongolia - and with a cargo train from Chernichevsk to Skovrodino in 2000.
On the Transsib I had to drain the petrol (but of course left two liters in) and they charged according to the weight of the bike, but is was cheap. Dont pay any money to the station boss for any permit, this is only to get some money out of you. Be early at the trainstation, ask if the train has a luggage car (in russian *baggage*) - than it should be easy and cheap.
For your ticket you will have to pay the tourist price, or find a russian friend to buy a ticket for you.
Park your bike in Novosibirk and Moscow only in guarded parking lots (stolyanka)
Email me direct for more informations in German.
Mika from Vladivostok - riding a XLR250 in Far East Russia and Siberia this summer