Does the manual transmission have the same issues as the automatic

Hello, Not particularly. The G25 transmission used in those was also used in many small Ford comuter cars, and certainly nothing very powerful. I've seen those transmissions last well over 200,000 miles with oil changes, but I've also seen them destroyed. The 2.0L and 2.5L 626 both use the same gearbox, and they both seem to hold up well in the absence of constant spirited driving.