The blocks are physically different castings to boot (obviously). But I would agree with wasinger's that they are "different". There's more major component differences than shared...i.e. pistons, rods, heads, cams, etc. Dimensionally some of those components might be identical but their physical make up are not the same.
The F150's 3.5 is designed to handle more torque and loads, hence the major forged component. The SHO's 3.5 is was not designed the same and I personally would have loved to seen those same forged internals in the SHO 3.5.
Not knocking anyone or their opinions here, just my observations.
So...back on the topic again...

I still believe the engine is behaving "normally" and there is possibly some minor hole in the tuning (i.e. fuel/timing/etc. tables) where under these unique circumstances it's seen.