Q: The car bogs down and stalls; and has a rough idle until the i tap the upper plenum.

If the problems started after you replaced the PCM, and the first PCM did not have any known issues, you might want to begin your diagnostic by re-installing the original PCM. Seems like you did a lot of work on the fuel system so be sure to replace the fuel filter in case the filter is plugged. If manipulating the plenum improved the idle, that would suggest a vacuum leak and you should check for vacuum leaks throughout including the EGR system, PCV system and so forth. Check the base ignition timing and ignition advance function (against Factory Service Manual specifications). Check for a restricted exhaust or a plugged catalytic converter (can check exhaust back pressure through port or infer backpressure by checking to see if intake vacuum is normal). After those obvious possibilities, an automotive scope would be used to look at secondary firing patterns in all cylinders to determine if the issue is fuel and/or ignition related and if so, which cylinders. If you want this stalling diagnosed by a certified Mechanic, dispatched by YourMechanic right to your location, please request an engine stalling diagnostic and the responding certified mechanic will get this resolved for you. If you have further questions or concerns, do not hesitate to re-contact YourMechanic as we are always here to help you.