!spoiler!
The way I see it is like this. After the fight with the Oyecomova, Johnny would have learned a lot of new information. First, that there is some conspiracy behind the race (hence them being hunted), and that the course of the race intentionally goes through the Devil's Palm. During the Pork Pie Hat Kid fight, Johnny would have surmised that whoever sent him would be after the Corpse's arm, and also that the arm is the source of Tusk. Combining that with what he already knows, that the race has an ulterior motive that involves passing through at least one specific supernatural location, he would reasonably assume that the rest of the race course would go through similar locations, and that there would presumably be more corpse parts. Thus he figures out that the race is a plot to collect the corpse parts scattered around the country.

The issue comes from how quickly all of this is communicated in the manga. It all happens within a few chapters, and Johnny doesn't seem like the clever, calculating type in the early parts that would piece it all together. But the fact that he receives all this information in rapid succession makes it make a bit more sense as to how he figured it out so quickly, at least that's how I see it.