The clues are all hidden in things he and people he knows would have in their possession. The Jesus and the Brides album he owns was straight-up given to him and when Comic Guy is murdered, the police officer doesn't put up much resistance to keep Sam away from the crime scene, where he just so happens to find the final piece of the puzzle.
Once Sam pinpoints the location of the cult, he sees that it's in a place that internet maps refuse to acknowledge, which is pretty conspicuous to say the least. He gets there, seeing the location is marked with the symbol for "Keep Out" that only homeless people understand and finds out that Jefferson Sevence faked his death and left several identifying parts of his body attached to an otherwise unidentifiable corpse.Now since we see this individual seemingly alive and functional enough to eat and have sex, he must have replaced the body parts he gave up. It's not too big a stretch to assume there's some kind of organ harvesting going on, with homeless people being kept as livestock. The Homeless King is confirmed to be complicit and kings aren't exactly known for caring about their people.
This then points towards Sam going from functionally homeless to full-blown homeless by the end of the movie. Since he was already a bit of a conspiracy nut before he got close, the cult would want to be rid of him before he could spill the beans, but if they moved too fast they'd risk an influx of questions that would embolden more like Sam. That's why the Homeless King let Sam go for now, because he needs to fade away gradually before he can serve his final purpose.