Dear brother if you are replacing the engine of a car which was initially having petrol engine, then it will consume more fuel because of gear box, as petrol engine gear box are high rpm, engine revolutions remains higher in petrol engine while diesal engines run at low rpm with same speed hence it will not be fuel efficient car if you install diesal engine with petrol engine gear box,
And regarding the auto and manual transmission, it is totally wrong that manual is fuel efficient.
Automatic transmission have low fuel consumption than manual one. If you will install the manual one on suggestions of mechanic, fuel efficiency will decrese more but it will not increase
Abdul Basit (Electronic engineer)