Here are the Rules I'll be using (based on combining many of the ideas provided by earlier posters). I'd love any suggestions beyond this:
Every level, a caravan not only receives a feat, but an attribute point as well.
Guard Job: +1 AC or +1 to attack.
Advanced Caravan Jobs: These jobs have a requirement of 6 skill ranks in the relevant skill, ability to cast 3rd level spells, or +6 BAB. All bonuses listed stack with related job (listed in parenthesis)
Chef (Cook): +1 Resolve
Coachman (Driver): +1 to Security checks
Warrior (Guard): +1 to damage rolls
Navigator (Guide): favored terrain (specific): +1 to caravan Security checks while in this type of terrain
Doctor (Healer): while in combat, fast healing 2 to the caravan
Hunter (Scout): favor enemy (specific): +1 to caravan attack, damage, and Security checks vs this creature type
Battle Mage (Spellcaster): gain the benefit of the Advanced Caravan Job you are acting as
Merchant (Trader): may spend 1 additional cargo unit during trade (and gain gold for each cargo unit)
Engineer (Wainwright): make upgrades to caravan while away from a settlement. If this is a Hero, this enables the Battlefield Repair Hero Combat action to repair during a combat.
Masterwork Wagons are available from the start of the adventure (stats are in the last AP)
Masterwork Wagon
Cost: 1,200 GP Hit Points: 40
Traveller Capacity: 6 Cargo Capacity: 6
Limit: None Consumption: 1
Special Benefit: +1 bonus to AC
Caravan attack is now removed, and replaced by the Hero Combat action described below. If no heroes are present, the caravan gets one attack.
Caravan damage increases at the same rate as that of a rogue’s sneak attack extra damage dice. At 1st level, 1d6, at 3rd 2d6, at 5th 3d6 and so on.
The caravan rule for the spell “Create Food and Water” is removed and the spell works normally.
Hero Combat actions: DC is set to 10 + the encounter level
Attack: The Hero may make a caravan attack against the enemy AC, up to four heroes may take this action.
Defend: The Hero may make a caravan attack roll against DC, to aid the caravan in repulsing the next attack, providing a +2 AC with an additional +1/ 5 points exceeding DC.
Rally: The Hero may use Diplomacy, Intimidate or Magic to rally the caravan against DC, granting a +1 Resolve check, with an additional +1/ 5 points exceeding DC.
Battlefield Repair: The Hero can cast a spell that repairs objects (such as make whole or fabricate) to provide the caravan with 1d6 hp per spell level (minimum 1d6). A Hero in the Engineer Advanced Caravan Job can use the appropriate skill to provide the caravan with temporary hp equal to the check result.
Summarized here