“though so shallow” means “although (the pits) were not deep enough” Here is a simpler paragraph: There are three holes in the ground around the pyramid. Each hole is in the shape of a boat. The holes are big enough, and have the right shape, so that boats could have fit in them, except that the holes were only deep enough to contain the lower part of the boats. Any parts of the boats that were built above the main deck would not have fit in the holes. Therefore, if the boats had anything built above the main deck, it would have been necessary to remove it before putting the boats in the holes (pits). [a “deck” is a floor of a ship. The “main deck” is the principal, most important deck.] One of the meanings of “joint” is the place two things come together and are joined (meet; come together; are connected). One kind of joint is where two bones meet. However, in other contexts, a “joint” can refer to where other things meet. Examples: A joint is the place where two water pipes come together; or where two pieces of wood come together. So in the sentence you are asking about, the word “joint” refers to the places where the casting stones come together, and where the inner chamber blocks come together. The work was done so carefully, that there are only 6 millimeters between one casting stone and the next, and one chamber block and the next. That is, the average size of the opening in the joints is only 6 millimeters.