Understand that, on your vehicle, there is no line from the 3/2 valves to the transmission modulator. When you first observe the system, you will see the supply vacuum split at the T and you will observe the vent lines split at another T, but these splits take the vacuum to the EGR system, independent of the vacuum control valve. The vacuum control valve is the white plastic unit at the rear of the IP and it has sole control of the modulator. It is the device that will be tuned to achieve the desired vacuum levels at the trans.

With regard to flaring shifts, if the vacuum is a bit high, it can be tuned lower and the flaring might be improved. If it isn't, the modulator pressure can be slightly increased to achieve the same result. All of these changes are tuning to overcome wear internal to the transmission.

Kent is not wrong when he advocates maintaining the EGR system. In theory, the EGR can coexist perfectly with the transmission modulation system, as it was when the vehicle was originally delivered. However, on a old vehicle with many items out of specification, attempting to maintain the EGR complicates the process, especially if any of the components in the EGR system are leaking in any way.