Warranty covers both transmission and clutch for 12,000 miles then just the transmission after that. It does not cover abuse , mistreatment or modification of the transmission. But it does not say that the owner is responsible for diagnostic charges to determine that it was one if those issues. It does require you to talk with the dealership owner or general manager to try to resolve it then Jeep will step in. Ask them to show you where in the warranty it says you are required to pay diagnostic costs. If they diagnosis the cause is one of those three and deny warranty then they should charge you for that and the two of you will probably end up in arbitration or court.