We just had to replace the transmission in our '03 Pilot last month, so I feel your pain! Are you getting any kind of warranty with either transmission? Yes, this is a known problem with older Pilots also. Have you gotten a quote from the dealer? Some dealers will give a discount (called "goodwill service"). We ended up going that route with a 3 year/36,000 mile warranty. The service manager said our engine could go for another 150,000 plus miles.
Good luck!
Tina