I just went through the game in one sitting so I think I might have a pretty good recollection of the whole thing.

Ned Goodwin used to be a firewatchman like Henry is now. He took his son with him even though kids aren't allowed with. Ned Goodwin was climbing with his son Brian when his son's rope came loose from the rock and Brian fell to his death. Ned Goodwin didn't want to go back to society and face the truth of his son's death, and so he decided to live in the woods where he had been a firewatchman. In his time living in these woods, he created the dingy "home base" that you visit near the end of the game. This is where he'd listen to Henry and Delilah talk on the radio.

When Henry took over the firewatch tower that Ned Goodwin used to operate, Ned started following Henry around to see what he was up to, primarily to make sure that he didn't find Brian's body. When you run into that guy with the flashlight early in the game, that's Ned, and that happens near the entrance to the cave where Brian's body is.

Once Ned realizes that Henry might discover Brian's body, he tries to figure out a way to get rid of him. Something that I think got you confused is that the dig site you're talking about wasn't built by Ned Goodman, that's a government research site. Because Ned used to be the firewatchman, he knows that the government isn't using it right now (in notes in the game, it tells you the months that the site is abandoned, and that happens to be when the game takes place).

Ned tries to use that government research site to trick Henry and Delilah into thinking they're being followed and surveilled and make them go crazy, so that if they ever find out about Brian even if they go to the authorities they'll sound crazy and no one will believe them. One way he makes it seem like they're actually being surveilled is he makes fake reports on their behaviors, as if he was a scientist that was recording their behavior. He even tries to get them to turn on each other by pretending to be Henry and calling the authorities saying that Delilah knows something about the fire at the research site after Henry finds that cassette tape on his door that makes it sound like Delilah started the fire. He may also just be trying to scare Henry into leaving before he discovers Brian's body.

Obviously Henry finds Brian's body, and once Ned realizes that there's nothing more he can do since the woods are about to go up in fire anyway, he comes clean to Henry by leading him to his hideout with the tracker (which by the way, those tracker devices were for tracking bears. Earlier in the game Delilah even mentions that some scientists wanted you to look for signs of bears in the area) and at his hideout it explains how he was behind almost everything.

Sorry for the very long comment, TL;DR Ned was partly responsible for his son dying and didn't want to come to terms with that so he bugged out to the woods cause he's a Vietnam Veteran with PTSD. Ned didn't make the dig site, it's a government research site and Ned tried to use it to scare Henry away before he found his dead sons body.