Update - Both left and right engine mounts were missing their securing nuts. Who knows how long the engine has been just floating on the mounts waiting for an incident like this throttle on/off/on event to rock the engine off the mounting stud. Perhaps the shop that lifted the engine out a couple years ago failed to torque them properly? In any case, not confidence inspiring... I'm going to go ahead and replace both mounts and use fresh hardware. Parts are on order. A little daunted by the exhaust/cat disassembly required, but we'll cross that bridge when the new parts arrive.
In the meantime, I lifted up the engine up off the engine mount stud and was able to reposition it so that it lined up properly with with mounting bracket attached to the engine. I secured the engine on both sides with temporary M12 flange nuts and some blue thread locker. Fan now lines up perfectly with the new shroud.
On first fire up after putting everything back together, there's no CEL but my GAP tool is showing two codes:
P0526-17 (Fan speed sensor circuit - General electrical failure - circuit voltage above threshold)
Workshop manual says: Viscous fan circuit, short circuit to ground, short circuit to power, open circuit
My next step: double check fan harness connection (fan is operating when engine on, so not sure about this)
P061A-64 (Internal control module torque performance - Algorithm based failure - signal plausibility failure)
Workshop manual says: Intake system air leak; Manifold air flow sensor(s) failure
My next step: double check intake connections from reassembly
Also, while I had the sump guard / skid plate off I checked the various drain plugs... found the front diff drain plug to be loose to the touch! Disaster averted. Torqued up now and awaiting the proper fluid for a drain + fill.