[HO455]

My Burban is lowered but not to the extent that the pinion is higher than the carrier bearing.
Up indicates the forward end of a shaft is higher than the aft end. The pinion yoke is considered the forward end of the pinion shaft.
Transmission 3.5 degrees down
Front shaft 0 degrees
Rear shaft 2 degrees UP <----- ???
Pinon angle 2 degrees DOWN

So my transmission yoke is lower than the harmonic balancer.
The front shaft is flat.
The rear shaft is higher in the front (so it is as you felt it should be, pointing up from the pinion).
The pinion yoke is lower than the pinion gear. Thus it is down.
I hope this helps.

"I guess it's my turn now.. lol". Hopefully your PO was more competent than mine was.