There will never be a definitive answer to this question, because an answer would require some reason or knowledge of what the people who first arrived in Jonestown were doing. It would also require some contemporary documentation of official actions taken by military and police officials in the aftermath. Neither of these is the case.
The problem with the whole death scene is that it was compromised from the start. The first people into Jonestown after the deaths – those who were there within the first 18 hours or so – were local aboriginal people and area Guyana residents, who removed some of the materials that Jonestown residents would no longer be needing. The second set of folks to come in were Guyanese troops, who were more interested in making sure there weren’t any survivors – or at least, survivors with guns — and less interested in preserving the integrity of the site as a crime scene. Even after the police arrived, any deliberate efforts to ascertain exactly what had happened and in what sequence were hampered by the fundamental need to remove the bodies as quickly as possible, given their rapid decomposition.
All of these factors are couple with the sheer scale of the carnage. Different counts of the bodies began at different places in the camp. The bodies were tagged and moved and retagged when the rain washed off the first marks and moved again when more bodies were discovered underneath the top layer(s).
The same is true with the body of Jim Jones. Photographs show him in different positions and in different locations. No one know who or when or under what circumstances it was moved, but it is likely the first person to actually do that didn’t know whose body he was handling. That would also suggest there was no malice or ill intent to the action.
Finally, the same is true about the gun that shot Jones. There are reports it was on his chest. But there are also reports that it was seven to ten feet away. But there are also reports it was a couple of hundred feet. So what’s the truth? The answer is, they are all probably true. Guns don’t walk around, and neither do dead people, but in the rough-and-tumble of the post-tragedy clean-up, very little stayed in its original position.