Its sounds like you are in Stone's headquarters now, correct? After defeating him once you should be able to follow him to an arena for another confrontation.
Try emailing support@larian.com, with a description of the problem, and maybe a link to this topic. You didn't mention Stone, so it is possible you may have run into a bug that can result in missing bosses; this problem is fixed in the second patch, but if it had already occurred in your save you will need to email it to Larian to get it fixed.
BTW, if you have a save before picking up those 4 stones and disabling the generator you may want to reload it. There is a fifth stone in the arena, and you need to use all of them at once to get a minor reward.
