If its distributorless, all that bottom gear runs is the oil pump. In earlier applications (distributored), the distributor ran off the oil pump via a shaft. So it was critical to get the crank, cam, and distributor all in line. It's really no different than a bigger cam-in-block engine, other than the fact that in the 2.3, the distributor runs off the oil pump, rather than the oil pump running off the distributor. Rather than making two steps in the timing process (setting the cam in line with the crank... then later setting the distributor), this is one BIG step.
In 89 I believe all the Lima 2.3's and later 2.5's were distributorless and just used that bottom gear for the oil pump. If you are having problems with your truck 99F150 feel free to start a new post, someone in this great forum will be happy to help you out.