Why would you try swapping the carts between motherboards when both were working fine? I'd certainly not recommend swapping SPI carts between mobos if you can avoid it. It's not like MVS. Have you swapped them back and they are not working on their mobos they originally had? If so I suspect you didn...
I would take off the battery, remove anything socketed then run it through the dishwasher. Make sure it's super dry before reinserting chips and testing.
Not cheap but I always use Novus. You can get a kit with grades 1 2 and 3 off Amazon. The three have different abrasiveness. Works a treat. Depending on how scratched it is you might not need all 3 grade.