I have an Outside Goodman 3.5 Ton Unit and a Evaporator 5 Ton Coil inside. My ? Is isn't this a mismatch system? My a/c runs for a long time before it cuts off.

Very much mismatched

Wow... someone was looking for mega humidity control, or was asleep at the wheel when installing. If the metering device at the indoor coil is sized for 5 tons, the outdoor unit will be somewhat overwhelmed by the rate of heat absorption at the indoor coil. If it is sized for 3.5 tons, the indoor coil will be somewhat starved for refrigerant under certain conditions. This may result in high superheat and a compressor that runs hot.