Engine skip/knock

In June 2013 on the way to Alaska our engine begin to skip/knock when going up hills. After several experiences of the knocking the check engine light came on. It had also been raining heavy all day. We were in Mitchell, SD and took the motorhome to A-1 transmission. They checked the codes and replaced the mass air sensor, air filter, and knock sensors ($900.00). They said the air filter was wet. After the repairs the motorhome has ran good until yesterday. While traveling through western SD and MT in a heavy rain the motor begin to skip/knock and the check engine light came on as it did in 2013. Today we drove to Great Falls, MT with very little light rain and had no problems. Would a wet air filter cause this problem and ruin the sensors? Any ideas what we should do? Thanks for all your responses. John