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Hello welcome to just answer I am master tech.
do you have the original harness off the 05 motor and the ecu ?
sounds like it's a wiring issue.
we have a guy at work that put a vtec motor in a late model civic and his has vtec and his had egr so their is a lot of configurations
im hoping it will work also.
but you are using a newer motor with new systems so kinda un charter waters here
the ecu is pre programmed and in order to do this you will need to contact a source like Hondata.