I would go back and have them go over the entire process of what they did to the car...
It sounds like they put the wrong model of transmission in it, the stock GT gear ratio in the transmission is 3.05.
You need to ask him what gear ratio the trans he put into it has, without telling him what it's supposed to be, and if he says 3.29 or 2.93, he put the wrong transmission in. Having the wrong gear ratio will cause all of the problems you described.
It could be fixed with a change to the PCM, the computer that controls the engine and transmission. Gas cap problem can wait until after the trans issue is fixed.
