My theory collection of ramblings:
This is all about something that happened in the past, that Danny (and Tom?) somehow were involved with or got wind of; a murder, an accident, something dodgy, involving most of the men in the town - perhaps to do with Olly's deadbeat dad, perhaps involving Nige's crossbow.
Everybody in Broadchurch is out and about at night up to various nefarious doings. This thing either happened, or Danny found out about it, in late March around the time of the paintballing outing. The vicar knows about it too, though isn't involved, and at some point in the past took the decision to "stand by" his parishioners and not let on; he can see everything from the church at night. This put him in a spot when Danny died, obviously, because he knows of a likely motive. But after Jack Marshall's suicide he decided he wasn't going to trust the police to do the right thing, and in his service after Danny's death he tried to let the town know that he ("God") would not "abandon" them. Now, with the handing over of the computer, he has decided he can no longer keep silent.
The "postman" Danny was fighting with was Mark, and he was involved in doing something that morning to cover up whatever the incident was. The boy on the cliff in the opening sequence is Danny, and he is looking stunned and scared because he is witnessing someone (the footprints on the beach below) doing something that clinches the proof of whatever the incident was.
As a sidenote, Psychic Steve is a practised con artist, who broke into the car in the Sambrook case, and quite possibly burnt the boat. The boat may be a total red herring and PQ may have been lying or mistaken about what she saw, not sure about that bit.