not entirely sure im a self taught DIY so I only go off experience lol

You've alot changed, even a new engine? Have you had it linked to an ECU fault reader?, checked engine and gearbox mounts?

suppose you'll laugh at me but have you changed the air filter?, checked for any air leaks? or checked the condition of the exhaust pipe? iremeber doing an exhaust on a 306 diesel as it was pretty much hanging off, made the engine feel shaky and powerless

do new injectors need to be coded to your car in order to work? not entirely sure about mondeos, i know my transit did.