2002 Yaris 1.0 VVT - Won't start!

[CTScott]

It definitely is strange. It really does sound like all of the key pieces are working. With the ECM (yes engine computer) I think you are correct that it is likely fine. I have seen ones fail where they work all except for an output driver for firing the plugs or injectors, but if they are all working it sounds like the outputs are fine. Also with you seeing spark and fuel it does sound like the immobilizer is happy.

The only other thing I can think of is that the cams are completely off in their alignment with the crank. Since the same mechanic worked on both of the engines, maybe it would not be a bad idea to have someone else verify that or take a look at the service manual yourself and verify that he has properly matched the marks on the cam and crank gears.