We have never played the Tunnel and the Plague, but it would be cool if the fleas could use the tunnel and appear somewhere very far away on the board.
The Plague can be played with small expansions, such as the Cult, with no problems. It does not react well to larger expansions as it is too diluted. Also, I don't recommend playing the Plague with anyone that hates house rules. There are a lot of weird situations, such as Halfling mentioned, that aren't in the book.
Playing with both Monasteries is too many monasteries in my humble opinion.