Flagstone kitchen floor (part 2)

At the end of one week, this is all we have completed. :( Some of the stones in this picture are bedded in mortar, while some of them are still loose. We have relaxed the tolerances on the grout joints a bit, so the grout will be more likely to flow into the joints (when we get to that part!). Because of the variations in stone thickness (3/8 to 1"), I'm finding it difficult (but not impossible) to keep the stones level with each other. Before the (thickly applied) thinset hardens, the thinner stones sink a bit. I've started resorting to shims made from scrap hardibacker to prevent this from happening. Seems to work.