Wiring harness difference
 

I'm jumping into an engine swap job Midway through. it was started by somebody else a year ago and left unfinished and that guy it's no longer working on it. I just swapped a different 06 engine into an 06 truck after its original engine spun some bearings. The wiring harness has a slightly different plug on it and I'm wondering what the solution is to make this work. I'm guessing that maybe the donor truck of the new engine was an automatic or some other difference from this truck which is a manual.

The main difference that prevented me from plugging it in is a little hook type thing on the corner of the plug that runs down the length of it that the trucks harness doesn't have. It looks like all the pins are in the same locations on the two different engine plugs so I'm guessing all the electrical stuff is the same. Is there a reason they put that hook on some to prevent you from plugging this in?like there's a difference in something else that will do damage if I were to shave off the hook to make it fit?
https://cimg2.ibsrv.net/gimg/www.die...a7de11cca0.jpg

I'm starting to see more differences than just this plug. Can I just swap the whole engine electrical harness and computer over or maybe just the harness? There are quite a few plugs on the new engine that don't seem to have a home on the truck and I was guessing they were all auto trans related until I just remembered that the new engine had a flywheel and clutch on the back of it, so it was a manual too. Now I don't know what to think. Both engines are 2006 and I don't know what other difference two 06 manual trucks would have had that would justify this harness change.