S3 engine bolts straight in, except the pressure plate needs to be changed. If it is an early S2a with the upwards exhaust outlet on the manifold, you can either swap manifolds or use a late S2a/3 front pipe. Alternator will require the wiring to be changed slightly - and if it is a pre-67 2a, you need to change to negative earth to suit the alternator, and probably not a good idea to run the charging current through the ammeter.

Carburetter and linkage may also be different, but you can adapt this fairly easily. Again, with an early S2a or a late S3, there could be minor differences in fuel line fittings, but easily dealt with.

John