The blocks are different. For simplest examples compare alternator, spark plug connections, and exhaust systems.
The newer version has:
1 more bolt points to allow newer plug system,
2 smaller exhaust ports to allow pre-cats to warm up faster,
3 alternator placement and wire system is different,
4 they changed from the clutch fan to electronic,
5 they also changed the belt tensioner system and routing pattern
This is just off the top of my head from when I wanted to do the same thing. If you still want to try it then you will need to change the heads to get the extra bolt points and smaller exhaust ports, you will also need to change out the mounting brackets to allow the newer parts to be attached (alternator, ac, power steering, etc), last you will need to change out the water pump to the newer one to keep the hp and fuel economy of the newer engine.
If you want to repair the engine instead then most of the time you just need a new head/head gasket set as well as new water pump, thermostat, fan, and fan relay (located under the passenger headlight).
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