You mentioned that you put holes in the pipes facing down. Did you drill holes? Usually with a bog you cut slits about a third of the way through the pipe. The slits are spaced a few inches apart. Facing up or down does not matter, people go either way. There is a sticky thread on bog building in the pond construction forum that may help. A little strange that you would be blocked up just two years into it. There are some people here that have never cleaned out their bog pipes. If the stones were the cause of the problem I would think that would have been right from the beginning. Maybe if you post pictures of the bog and if you have pics from when you built it there might be a way to figure out the issue.