I have an 89 honda with an ls swap, and it was running fine then the one time when I go to start, I turn the ignition on to auxiliary not trying to start it and the main relay clicks until I turn the key off. I replaced the main relay and fuses are fine. What else could be the problem? Thank

If the CEL stays on, the ECM may be bad.

What's the CEL?

Check Engine Light.

Perform the K-Test on your ECM:

The K-Test: Remove the MAP Sensor connector and turn the ignition switch to ON (Position II). Using a multimeter, check for 5 volts going between the MAP Sensor connector's reference wire (+) and ground. As you look at the connector, this is the socket on the right. Really press the black test lead into a cleaned main ECM ground on the thermostat housing. If the voltage is low, it's probably indicating ECM failure. Most failed ECMs will record a fraction of a volt. To me, the K-Test is simple, elegant, and accurate.

All right thanks

OK I had another ecu and its still doesn't start. What else could it be

Is the "new" ECM any good?

Yeah