Could the motor sound be something like the alternator or PS pump? Maybe one of them is failing, causing an intermittent drag on the engine. Stab in the dark on that since nothing is coming to mind that would be a motor. It's not like our trucks have ABS systems or anything.
BTW, there is also a timer that controls the cold start injector that can fail.
From the sound of it I might check the EGR and IAC, although an intermittent O2 light might be a clue. If the ECU is chasing a variable O2 feedback that would also explain the poor running at altitude.
'91 Pickup - Imelda
'08 Tacoma TRD - Donna
'09 Kawasaki KLR650
'12 Gunnar Rockhound 29
"To live is to suffer, to survive is to find some meaning in the suffering." -- Friedrich Nietzsche