I noticed (and then forgot) this when I first installed the engine, but the rear seal across the vertical sheet metal does not lie close to sealing along the sides. Did I install the rubber upside-down? The shorter flap is on top.

Looks correct but you need to coax the back flap to the Trans side of the R. tin

The engine tin fits between the two flaps, one flap in the engine compartment and one in the transmission section.