Until sometime during the K1, when the 2nd factory was opened (hurriedly), the frames and engines were made and stamped: that was all. They were at different facilities until they were mated together on the production lines. If an engine showed up something undesirable during the test run or test track circle, it was pulled and sent back for rework, and the near-complete frame went to a rework line for another engine. This was how so many bikes ended up with things like K3 switches on K4 handlebars, K1 kickstart arms on K3 bikes (which had bigger rubber cushions), and the like.
This info came to me from a Honda rep I knew (Randy, don't remember his last name, but might if I dwelled on it...) in the early 1970s when I had my shop and these questions were everyday stuff: he had been to Japan twice by then and had seen the facilities live.