This level was a real puzzler. So many things did not work one time, such as delivering the girl to the LZ for pick up but no helo showed up, and did work at other times (she got picked up by the helo)! I had to restart the level twice when the save game function became corrupted and would not load blowing all that work. I learned that you can complete the level even if you don't finish some of the functions such as "Find Evidence", deliver the girl, don't report the arms cache as the priest requests, blow up the guy's house.
To destroy the main base,
Mission completed! Then it was the trip back to Manhatten base which was being evactuated. That is when you do the mission to get the documents at the house where you have to kill off insurgents and blow up the house. I used the satchel charge, flattened the house and it did not show up as complete in the map notes! But this does not seem to stop you from returning to Manhatten and completing the level.