Why did my fuel pump stutter after it was installed into my jeep?

Must likely, the lines were air bounced at the time. What you are telling me that when the shop replaced the filter and the filter in the tank was the only filter...that's not true. The tank usually has a type mesh filter to clean some particles but should be a cylinder shapep type gas filter somewhere on the delivery line of this vehicle. You must replace that one as well. Good luck...!