This is actually an easy fix.
When you change out to a newer motor, you have to do a few things to make it work.
1.Change the reluctor to the original one from your vehicle.
2.Change the cam sensor to the original one.
3. make and install an egr block off plate if yours did not have one.
4. Use the original instake and connectors if different.
I did this to my 2003 Liberty to a 2007 motor and it worked perfectly.
Drives like a new car and I now have 2000+ miles on my swap.
Good luck and good driving. You will enjoy your Liberty.