It's weird but the port drive lags behind the other one by a half second when going up or down., what causes that?

Slow pump might have more resistance in a wire or conection.

Where are the best points to meter that?

Check to be sure both pumps are pulling the same amperage.
Be sure the wires running to the pumps are the same size and length from power source.
And check to be sure all the hydraulic lines are all the same length.

Any variation will cause a difference in performance.