You made no mention of what year the motor is. If it's a newer year motor 99+ more than likely it's the fitting for the MAP sensor. Although I'm not sure if it's truly threaded. The map sensor has a ribbed rubber seal that gets inserted into the manifold and the sensor is held in with a torx head screw which should be the smaller hole adjacent to the port. That hole isn't tapped through, so you should have no problem with having to plug that one.
If it is indeed a newer manifold, you have two choices, use your older manifold if you still have it or figure out a way to plug this one since you don't need it on a 1990. A new map sensor is around $35 if you didn't want to fuss with trying to figure out how to plug it. Stick in what should be there and forget about it. I would opt for the correct intake though, jmo.