I am in agreement with
@Billet1500 4x4 regarding the post-speaker swap ANC problems being caused by polarity problems... and I also believe the vehicle wiring has something to do with it as I had ANC problems before swapping anything.
Recap: I swapped all six base system speakers using Metra harnesses, connecting the positive white lead to
what was supposed to be the positive truck wires, and have found polarity mismatches around the cab.
Using a program called “Speaker Pop” on my iPhone (buggy but it works) I confirmed I have two speakers in-phase (right doors) and four out of phase (entire left side, plus the right dash). I will report my findings after confirming all six speakers are in phase and the ANC is reconnected.
FYI regarding releasing pins from connectors, although I used a sewing straight pin, you can buy little tools that release those pins safely without damage. The tools vary in size, not sure which one is correct for the amp connector under the seat but it would be small, around 1mm-ish.