I would run across the head bolts to verify they are still properly torqued. It makes perfect sense that the intake, valve cover, and oil pan bolts were a little loose. What you are experiencing is the gaskets relaxing a bit, so no big deal. Just torque them down one more time and be done with it. Since there are no gaskets at the main caps and rod bolts, if you torqued them down properly in the first place, you shouldn't worry about them. And if you used factory style self locking rocker nuts, they didn't loosen either.