I would have to see data from the car at the time the misfires occur in order to narrow it down to a specific thing or at least to a specific system.
RPM
TPS
AF Sensor Lambda
AF Correction
ECT
IGN Timing
Knock Correction
Roughness on all cylinders
Rear O2
AVLS both banks
Batt
Here's my theories in the mean time.
This generation still maintains a light throttle fueling. So there is a difference between OFF the accelerator and barely on it. Any slight movement of the APP tells the ECM you are on the throttle. And that brings to mind the APP feedback and range performance.
If the timing belt is stretched, or the tensioner is weak, when off throttle and during engine braking the timing will be off. Think about the connection to the converter and a locked TCC. Like letting off the throttle with a manual, the crankshaft gets a brake affect and is slowed quickly, (this is one of the reasons that belt guard is over the crank gear on manuals). With a loose belt the cams will be late to follow suit and the piston movement against the valving changes the engine's breathing and combustion chamber pressure which can cause imbalance on the crankshaft. But this doesn't flow with the fuel cut off throttle because the engine is an air pump and the firing spark plugs are just firing without really burning anything. So something is causing an imbalance.
If timing is the case, then when the crankshaft "kicks" off throttle from the engine braking affect, that would give the ECM an erratic signal and it would think it's misfiring off throttle. On the same token, if the crank and/or rod bearings have wear, that excess movement would create the same type result, an imbalanced engine.
Leaking fuel injector comes to mind, but since you've swapped them, that may be ruled out. Unless the fuel from the leaking injector is traveling to the other cylinders via the manifold runners and off throttle the cylinders continue to get fuel but just in differing amounts this would create a scenario for a misfire with one or two firing while the others are leaned out. This is where Lambda measures come in to play to see if the engine is really in a fuel cut mode, or it's still getting fuel, or it's not cutting fuel for some reason related to a sensor feedback issue. OFF the throttle, as
@plain OM posted, the Lambda goes to 1.4 indicating extreme lean out and this is normal. If you are watching AF Stoich, then it would be 20-21 AFR. If it's not, the cylinders are getting fuel either due to injector(s) issues, or sensor(s) feedback.
Keep in mind, a single injector can fail and the others be okay. On the flipside, the injectors have been operated equally throughout the life of the engine. They get the same fuel, the same maintenance, same operation. You could have a full set that have issues and your moving them around isn't necessarily proof to discount one or all of the injectors.
Now,
the most important thing on the car has not been checked. At least I didn't see it in you posts.
Battery and Grounding
Do you have a Midtronics battery conductance tester and do you know how to use it to check the cables and various ground points? The main ground is good with no more than a 50 amp loss between the negative battery post and the lug at the end of the ground. You do not want any more than a 75 amp loss between the negative battery post and the alternator case.
Plenty of times there have been posts on this forum where the grounding was causing issues. The grounds are the way the computers communicate and operate their outputs.
Lastly, what codes are stored on the other modules on the car? All of them. Did you run a full scan of all the computers?