I wouldnt be that sure the water is getting in through the stone. And even if it is it might not necessarly be the stone guys fault. It would depend on the detail that the engineers specced, if the stone lads done it to spec then they would be in the clear. You say the roof is wet and the walls, it sound like the water is getting in at roof level and seeping down? What is ove the bay window? There should be a flashing detail allaround the window which should keep the water out. Sealing the stone itself would not be best way to keep water out, it would be a simple action but not effective in driving and consistent rain.
Dont mention the small claims they will prob laugh at you. Get your engineer to have a better look at it or get him to get someone who knows. He did sign off on the work