If you have any way to datalog your truck, take a look at what your cam phasers are doing when this happens. Cam position is a real cornerstone of EcoBoost Ford tuning, and will determine which ignition timing tables, load limit tables, volumetric efficiency tables, etc. are being used. Cam phasers use oil pressure to advance/retard the intake and exhaust camshafts. If oil level is too low, oil pressure could be too low to properly actuate the phasers, throwing all of the downstream systems out of whack.
The VCT system is highly variable depending on driving conditions, so it's hard to say what sort of cam position you should expect at 'x' load, 'x' rpm, etc. BUT, if you see that VCT-E Actual and VCT-I Actual positions are stuck at 0* for a prolonged period, you can assume that the phasers are not operating correctly.
I know any mention of cam phasers can cause panic, and that's not my suggestion here. Rather than the phasers themselves being faulty, I would bet that low oil level or oil sloshing away from the pickup (and therefore low oil pressure) would be the culprit.
The Raptor does not use a MAF for measuring airflow (they operate on a speed density strategy), so I would not bother with that. Throttle learning is, in my opinion, unlikely to be an issue. But throttle behavior is also something that you could log to double check that theory.
As a testament to this theory, I saw a datalog of a vehicle where the phasers were stuck at 0*, and final highest individual cylinder ignition timing was some 8-10* less than what you would expect to see on a normally operating truck. That represents a HUGE loss in power - these engines are extremely timing sensitive for power. And it all boils down to the cams not being phased as expected/appropriately, and different ignition timing tables being used that commanded drastically less timing.
No promises that this is the issue, but it is certainly something to check! Let us know what you find!
Best,
Sam@Cobb