To install the 1995 Civic engine in a 1999 Civic, you will need to make the following modifications:
1. Swap the intake manifolds.
2. Swap the exhaust manifolds.
3. Swap the throttle body.
4. Swap the fuel injectors.
5. Swap the distributor.
6. Swap the ignition coils.
7. Swap the spark plugs.
8. Swap the engine mounts.
9. Swap the transmission mounts.
10. Swap the axles.
These are just the main modifications that need to be made. There may be other small modifications that need to be made as well. It is important to note that this is a complex and time-consuming process. It is recommended that you have a professional mechanic perform this installation.