Been driving my truck two to four times during the week, to my work and back home. I am going to check fuel filter and DCA tomorrow. Will let y'all know more. Once in a while, engine shut down all of the sudden. I suspect CPS is flaky. Will replace it tomorrow. Have new one on hand.
Other than that, I am monitoring the vibration/stumble. When I change the gears, I pushed the clutch pedal in, it still vibrates. I would say that the transmission is not the issue but something else.