I agree that the terminals were probably put on with the wrong polarity.
Some electrical damage has probably been done but bear in mind that the thick lead coming from the Alternator to the Positive side of the battery has a built in "fusable link" inside the cable....near the battery end.
Remove this thick cable on both ends and check for continuity or else with the engine OFF the cable at the alternator end should read +12 volts with respect to ground if the fusable link has not blown!
Also check the cable harness behind the Fuel Filter Mounting Bracket as mentioned as it is a known problem that chaffing to chassis of the harness may happen on the 2006 CRD!
You can download the 2006 KJ Service Manual here..includes Circuit Diagrams.
http://www.colorado4wheel.com/manuals/Jeep/KJ