Car battery burnt out my alternator when I put the positive cable on 1st. then the neg. 2nd.?

This era a ford vehicles has been known to melt the large 3 wire connector at the alternator. Most replacement alternators come with this pigtail and require it be replaced for a warranty to be valid. It is quite possible that a short in this connector was the cause of the battery failure in the first place. Replace the alternator and connector and be sure the cables at the batt are connected properly. Should be no damage to the ECM but you can never be sure until everything is reconnected.