1) The cost of a Motogp prototype is much more than a tuned race virsion of a street bike in WSBK.
The days when a WSBK bike was a tuned street bike are long gone.
The costs of running a top WSBK team aren't as much as running, say, HRC or Yamaha Racing, but a lot of the development costs are hidden in general factory R&D and machining, where the GP bikes budgets are one cost centre.
There is little on a WSBK bike that is 'stock' - think of it more as a silhouette class... one that looks externally a lot like the bikes you can buy for the street.
In reality, there is little on a WSBK that is the same as a stock bike - swingarm, suspension, exhaust, wheels, brakes, engine internals, cooling, electronics, fuel delivery, fuel tank, fairing, seating, controls, handlebars and footpegs. As well as that the materials are significantly different with carbon in place of plastics, titanium in place of aluminium alloy on a production bike, except the sub-frame - it has to be the same material as stock, or heavier and no carbon/kevlar in the swingarm.
What stays the same? Air box, fuel pump, the number and placement of exhausts, chassis - although it can be strengthened with gussets and tubes, dimensions and position of bearings in steering head, engine mounts, swingarm, suspension, "Fairing, mudguards and body work must conform in principle to the homologated shape as originally produced by the manufacturer. "
If you are interested, the following details the differences between a WSBK bike and a stock bike - over 30 pages of technical regs/allowable mods.
http://www.fim-live.com/fileadmin/alfresco/6510004_Anglais.pdf