The stones were shaped by hand, primarily using harder rounded stones (often quartz river cobbles), and I've seen a number of these in the stone quarries. They also used some bronze tools to extract blocks, but the shaping involving battering the blocks with the hammerstones. Moving the largest stones involved dragging them with ropes, and often required a thousand men or more. They only moved the largest stones over short distances of a few kilometers. The stones they moved up to Ecuador were still quite large, but only up to about 700 kg/1,500 lbs - these I suspect were carried on something made from wooden poles, like a litter. Archaeologists and other researchers have done quite a bit of work on these questions, and there is plenty of historical and archaeological evidence to show that the Incas were quite capable of doing these things using very basic technology in combination with the labor of many thousands of their subjects.