My take on what it all means (spoiler)
First off, you'll have to bare with me, here. This was an incredibly cryptic movie. There are a lot of things I just don't understand about it, but let me try my best to map out what I think you guys in the spoiler thread missed. At the end, when John is talking to the FBI agent, the agent says a large amount of money was transferred into his account. Now, he was left with one suitcase with some undescribed amount of money in it. What if that money was so he could take the part of Neely. Neely paid him to take a single suitcase (perhaps the one he was left with when everyone else went to the other side). So John is supposed to pass on the favor by offering someone who needs help the amount of money that was in the suitcase if they'll take it out to Cowboy in the desert.
We see that John gets the bandage on his neck, probably from where they extracted his sperm. Maybe Neely had the same thing, and that's why he wore the neckbrace. Knowing you got abducted is enough to drive anyone crazy.