I checked your son's website, and he has followed the same trail I followed and possibly ended up in the same place. Your son's weblog describes Colon very accurately.
I went to the Shipping Office in Colon Panama. Check here first and see if they have a "record" of your son "possibly" finding a boat that will ship his bike and himself. There will be no written record but someone there will remember. The top guys will be honest, they are on good government salaries, and will tell you.
About two hundred meters from the centre of town there is a dock for small boats. The guys that run out of there (to my disdain I didn't find this out until I was aboard one of these boats) run contraband into Colombia. I paid for passage to Cartagena, but got "dropped off" in Monito near the Darien Gap. I can possibly find my boat receipt for the name of the boat, and photos of the Captain and a german guy who calls himself Andre (runs 50% of the contraband) if your investigations point toward this being what happened.
The German guy got me in piles of trouble in Colombia by politicking among some unsavoury characters and trying to extort money from me. (German guy not a Colombian). He had told me a story on the boat about he used to be a lawyer in Germany and about how he had been married 11 years, met his wife 13 years ago and she was now having her 24th Birthday. Do the math on this pig. Also stated his real name was not Andre but would not say what it was.
It is unlikely, but just in case, if any information points toward this route please let me know and I will give you as much info as I can scramble up.
If you find the lad, please post so we can set our minds at ease. I think I speak for all travellers when I say we all feel terribly moved when we see a MP posting.