in the early '90's Ford moved them around a bit, the first iteration was with right where the distributor would be and the other right in front of the exhaust manifold (I know this, I have two engines set up this way, works fine), after a while they moved them around, I think there was a bracket to put both on the drivers side behind the alternator/power steering pump and another that put them both on the passenger side. The wires are only so long, if it's mounted under the intake, that's where that harness was designed to put it
it most likely means you have a slightly newer engine, probably a good thing