Chrysler Repair: 2005 T & C 3.8 to 3.3 engine swap

Question
I swapped a 3.3L engine into a Town and Country that originally had a 3.8L engine.  The 3.3L has and EGR valve and the 3.8L did not.  The 3.8L had a knock sensor and the 3.3L does not.  The ECU appears to be somewhat confused.  The engine ran for a while but threw codes relating to the missing parts.  Now it locks out the fuel injection when you try to start it.  I found a 2001 engine wiring harness would that work in conjunction with getting a 3.3L ECU or can I have the old ECU re-programmed to work with the 3.3L engine?

Answer
Hi Scott,
What is the year of the vehicle from which the 3.3L was donated?
As to 'locks out the fuel injection', that would more likely be related to the vehicle theft security system being armed not the fault codes due to the engine swap. Try again to cancel that system using the door key in the passenger side front door lock.
I don't know about reprogramming the ecu but I believe there are companies that specialize in selling ecu's and so check with one of those, on-line. And an '01 harness is likely quite different than is on your '05 vehicle, is the 3.3L originally from an '01 donor?
I have wiring diagrams for '98, '02, '04, and '05
I just found your question in the "pool", sorry for the delay.
Roland