Unless you replace the engine with the exact same make and model you will more than likely have to remove the old engine mounts and glass in new ones. You also want to check if the rotation will be the same or else you need a new prop. Exhaust, water intake, etc, etc, may have to be modified/changed depending on location of things on the new engine. A lot of people have reported that the cost of installation has equalled the cost of the new engine.
SV Laurie Anne
1988 Brewer 40 Pilothouse