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All due respect, you're certain to have a better grasp of it than I do. Integrator delay jumps to top of mind. I haven't thought about closed loop PID tuning for a couple weeks now so it's sort of fuzzy for me, but it seems like it would be easier to fine-tune without having to reflash the ECU in between changes. O2 switching threshold may be another good candidate. Long story short, tuning a PID control loop such as this is a complex subject requiring a good bit of knowledge to master.
Don't take this to mean I'm asking you to go off on an adventure trying to code things for my whimsy, I respect your time and I'm absolutely not asking that. Think of it more like I'm thinking out loud about what I perceive as the most difficult things to tune.
I'm relatively sure that a stable closed loop idle with headers and a moderate cam (more than 30 degrees overlap) is going to be more or less un-obtainable. I thought I was relatively close with my setup, but I've yet to get a wideband so have no other benchmark to go by other than the seat-of-pants dyno telling me it's relatively smooth at idle with the a/c on.
I think the biggest challenge is closed-loop operation between idle and your cam's lowest advertised torque spec (i.e. use with xxxx rpm stall convertor). For me that's about 2200 rpm, which is basically the entire cruise range for my particular engine / chassis. It's my theory that integrator oscillation in this range is my biggest source of false (and / or not so false) knock events.
My O2's read rich, my Wideband says lean.