Thanks hanky,
Yeah, I only pulled the positive cable from the battery to verify what I thought was happening which is the alternator is not powering the engine. Does anyone know is it common to have to flash an ecm or pcm on a Ford escape after changing out the engine?

 

You may get some different opinions on this,
If you install the exact same engine with all the original electrical components the system has been working with, the computer doesn't know the part was removed and reinstalled, but if you install any different sensors, you may need to tell the computer a change has been made.