The bike shop wants to charge you $3000 for the pistons, and $400 for the dismantling of the engine. And a later $4000 for the so called 'storage fees'. Nice. A bike shop that services MotoGP bikes, perhaps?
If you can, borrow money to get your engine repaired. The lay it up and sell it. If you are able to fetch a reasonable price for your spec 1, it should leave you with enough money to go back to the bike shop and negotiate with them over the 'storage fees'.
Although negotiate isn't exactly what I'd do if I came across such a bike shop.