Anferney, You should have a spark plug order stamped on top of the plenum right above the ignition modules. The firing order may be 1-2-3-4-5-6, but that doesn't mean the wires need to be plugged in that order. Look at the attached diagram for the order in which the wires need to be plugged. But make sure to check the stamp marks on top of plenum.
As far as your questions about reversing the wires - that most likely cause the hickups and the symptoms you describe. What happens is the spark occurs at the wrong time. It may be happening that in one or two cylinders the spark occurs when the cylinder is on the exhaust stroke. In this case the fuel will be burning up when it is in the exhaust manifold - thus the cherry hot manifold.
The system used on these Montero engines is the "waste spark" type. This means that both cylinders connected to a single ignition module fire spark at the same time. So theoretically if you were to reverse the two wires that were originally connected to one module, you will not have any adverse side effects, but switching between modules will cause trouble.