First: Get color photocopies of everything. Take one set, leave the rest with friends so they can fax you them if necessary. Or just scan them and leave them in your gmail account. This is just for backup purposes.

Second: You are overprepared and overconcerned. Rejoice in this fact, life in Latin America is way less structured than you expect.

There are two kinds of stops you will experience: Border crossing officials and random cops trying to extort money from you.

For border crossings, you will need: Passport (original), International Driving Permit (original), vehicle title or registration (original or color photocopy, doesn't usually matter but carry the original just in case). You will also usually need photocopies of one or more of these documents (and sometimes copies of documents they give you). Carry a half-dozen black-and-white copies of your passport (picture page), IDP, and vehicle title - at about 2/3rds of the border crossings this will save you a trip to the photocopier.

For random cops you will need your originial International Driving Permit. Carry 2 or 3 of these, they are super cheap to get. Sometimes they will threaten to keep it until you pay a fine. That's why you have more than one. Let them keep it and ride off. I never had a traffic cop ask for a passport.

There are odd stops that require showing your passport (ie, checkpoints in southern Panama if you go there). Show them the original, no big deal.

All the other items are superfluous. Unless you're bringing a small pharmacy (you'd have to have a pannier full of pills for someone to take notice), whatever certificate is pretty much irrelevant. Nobody ever asks for vaccinations. Travel insurance is between you and the travel insurance provider, the locals won't know what that is. Don't take your birth certificate, it's just one more thing to ruin/lose.

Relax and have a good time - it's going to be great

Jeff

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SF to Panama and back
How I Nearly Killed My Friends In Baja