Why would replacing the AFM not help at all in this situation? I am up for correction if my logic is incorrect, but the computer is seeing 16,000 Hz coming from the AFM, when it should be no more then ~160 Hz, while the TPS is reading no more then 5% open, coolant at normal operating temps, and RPM at idle speed.
I didn't know what the mod was called specifically, but I have run the vehicle with an inline fuse and toggle switch wired directly to the battery and fuel pump with the same problem. Currently I am running the fuel pump with the toggle switch still, but power pickup is now at the ignition hot terminal on the fuel pump relay wiring but no relay is involved. I would have mentioned this before, but I didn't think it could cause this problem to be honest.
Could over retarded timing cause some of this issue? Just thinking out loud here, but too far retarded timing could cause loads of unburned fuel to be pushed out of the cylinder giving the afr a false rich signal, the spark plugs to be clean as the spark would be too late in the combustion cycle and mostly used as burning off fuel that stuck to the plugs, and the cut out at high RPMs because the spark is too far behind the combustion cycle and the engine literally tries to diesel with too low of compression. Of course the only thing it doesn't explain is the weird signal I am reading from the AFM, but the other symptoms seem to fit or at least they do in my thinking out loud. I checked timing once before and it was fairly close to what the TSRM called for, but I hadn't taken into account for the longer duration and larger lift of the cams. Maybe? Its an easy thing to check for sure.