98 Cobra uses coil packs/plug wires, which will not be compatible with 03 harness.
if you swap over to COPs, you will need to get some 99-04 cam covers and the COPs will not fit the older style cam covers.
The IAT, IAC, TPS and ECT sensor connectors are also different from 98 to 99-04, so you would need to either swap the 98 units out for the 99-04 units, or splice in the older harness connectors.
98 has IMRCs, buy you can get some IMRC delete plates.
This is just off the top of my head.
if you swap over to COPs, you will need to get some 99-04 cam covers and the COPs will not fit the older style cam covers.
The IAT, IAC, TPS and ECT sensor connectors are also different from 98 to 99-04, so you would need to either swap the 98 units out for the 99-04 units, or splice in the older harness connectors.
98 has IMRCs, buy you can get some IMRC delete plates.
This is just off the top of my head.