Ok, first off is that the engine block can not be based from a stock production machine. It must be sole purposed for MotoGP. WCM already was penalizied this year for using a stock R1 block. Here is the rules on engines..
Engine capacity: max 990cc, Cylinders: min 3, Weight:
min 135 kg for 3 cylinder
min 145 kg 4 or 5 cylinders
min 155 kg 6 or more cylinders
and I think its an extra 10 kg for oval pistion bikes, but currently there are none. Current configurations are...
Honda RC211V - 4 stroke V 5
Yamaha YZR-M1 - 4 stroke 4 cylinder
Aprilia RS Cube - 4 stroke 3 cylinder
Suzuki GSV-R - 4 stroke V4
Ducati - 4 stroke 4 cylinder V4
Kawasaki Ninja ZX-RR - 4 stroke inline 4