Give us an update on what you've tried/results bud. I see from your sig that you've installed the upgraded MPFI spider. That should've also helped idle smoothness.
Thing that's stumping me is you only developed this issue after you swapped to the 0411,....leads me to think it's linked to wiring or PCM/tune issue.
Before doing the OS/tune swap in the PCM,.....check to assure a pin/wire connection at the PCM Didnt work loose during your 0411 swap. Check all your ignition related wires for any looseness,....with an ohm meter (if you can). Pull both connectors off the PCM and look at each pin (on the "connection to PCM" side) and assure one of your pins didn't get pushed back up into the connector,....you should be able to see the silver pins butted flush up with the end of the connector (all equal).
Do this test with the meter set on the "ohms setting", not the "continuity" setting.
I'm sure you already know how to do this,...if all looks good at the PCM connector end (all butted up/none pushed back up in the connector) disconnect the wiring/pin from the PCM connector, then pull the corresponding sensor/end connector and slap a meter between them,...while slightly wiggling the pin on the PCM end (do same on sensor/end connector),.....that'll test if the pin has worked loose/not making best contact,....your meter reading will jump all over the place if it's a bad/loose connection,...or show higher reading if there's any corrosion (per below).
When testing on a good wire/pin/connector, the "ohms setting" will show a steady/close to zero ohms (may show 1-3 ohms, which is ok),...but anything more than this would show a possible corrosion issue in the wire itself (hole in the wire insulation somewhere), or corrosion at the PCM pin or sensor end connector. If meter reading jumps all over the place, while your wiggling the wires/pins/connector,...it's showing you have a loose connection. And, of course, if no ohms reading during testing,...... sum-ting-Wong (broke).
Let us know how you faired out.