Now I'm going to contradict myself and actually post a long post. Please note that this is entirely my own opinion.
This is my biggest problem with a lot of the well ER said something mean about MR talk. First, as has been pointed out innumerable times, this was not right after the fact, it was something like a week later. Also, quite frankly, although MR has been a bit less direct in his approach, he's certainly managed to get in more than a few digs at ER, as have many people.
Secondly, for Lord's sake, this is your child we're talking about; your baby. I have thought about this a lot, and I don't care if your ex said you were Beelzebub himself (and she did not) -- very few people are divorced because they love each other. Put that aside, stop worrying about what people think about you, or whether they're talking about you -- of course they are -- you saw your child last, unfortunately you have a record that is easily accessible via the internet -- one which is ultimately no one's responsibility but yours, and you've made some verifiable mistakes in your personal life. I do not care, I really truly don't - none of that taken alone would convince me of anything.
From day one, take the Mark Klaas route -- deliver yourself to the police, take their tests, provide a full description of your activities, eliminate yourself from the equation -- it may be unpleasant, and it may hurt, but do it. This is your baby.
Then get yourself in the media -- even if you are shy, even if some of their questions about the past are hard. Participate in searches, stand on the shore of the lake when they search for your son. Yes, people are going to be looking at you, yes, some are going to think you are guilty, but if you know in your heart you are innocent, let that truth protect you.
Parenting is hard. Being a parent of a disappeared child is unfathomably so. But this is your child, you helped bring him to this world -- he needs his father to help him find him and bring him home, whatever the situation may be.
Again, IMO only.