Doubt it,the ecu will be coded to the key so will need recoded,you are saying the pipes are different as is the engine code so I'd say its a safe guess there are other differences.
I bought heated seats for a 54 plate mondeo st,the seats were from a 55 plate,plugged them in and they were hot all the time,turns out the looms changed across the years and could have caused airbag problems too so just because it's a 1.6 tdci doesn't mean it's the same thing.
The 1.6 tdci is bad enough without giving yourself more hassle.
What was wrong with the old engine and did you get the new engines turbo?