After finding so much water in the intake tract I was worried about what would be unearthed as I dug deeper. The design of the upper intake makes it hard to see into from the engine bay. I aimed the camera of my iPhone down the hole and snapped a picture, here's what I saw:
At this point I didn't think we were in too bad of shape. The intake incorporates a flap that snuffs out the engine in the case of a runaway or "dieseling" effect. You can see the corner of the flap in the bottom right corner of the intake. Most of the gunk inside of the tract was loose gasket material and carbon buildup.
With the upper intake manifold removed you can see the damage to the blower vanes. Unfortunately water had leaked past the flapper and down into the aluminum vanes. The blower was full of mold and worm holes from being eaten away. At this point there was no hope in getting the bus to run at its current location.
After removing the blower completely We found that the block was fairly dry. The only internal damage that was visible so far was a little stream of rust water coming out of one of the cylinders. My guess is that the lower end of the block is indeed filled with water. At this point our plan is to get the bus home and do a full teardown.