I have a 95 honda civic that won't start. I have to turn the key on and wait for the check engine light to go out. It can take up to an hour before that happens and the fuel pump finally gets power. I have replaced the main relay and checked all of the fuses. It still has power going into the relay but not out of it to the fuel pump until the check engine light goes off. I have heard it could be something to do with the ecm or the ignition switch, but I don't know how to check them to see if they are bad. Any help would be appreciated.

Your Civic shows classic signs of ECM failure.

. Perform the K-Test on the ECM:

Remove the MAP Sensor connector and turn the ignition switch to ON (not start). 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.

. Replace the ECM, if warranted by the K-Test:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-selected-other-vehicles-46563-3.html#post235038

Easy fix.

I checked the map sensor and it read 5 volts. Then I left the positive in the map sensor and connected the ground to the main ecm ground in the thermostat housing. It still read 5 volts. I don't know if I did something wrong or if it is something else.

Have you performed the K-Test, when the CEL stays on? That will help you determine if you're experiencing intermittent ECM failure.

When I checked it earlier the cel was on. I was connected to the positive wire on the map sensor and I put the black lead to the green ground wire on the connecter to the thermostat housing. I was getting 5 volts through it.

This is leading in an unusual direction--to the ignition switch. Check the ignition switch for wear, pitting, or melting.

Honda Civic Ignition Switch Replacement

1. Disconnect negative battery cable.
2. Remove dashboard lower cover and knee bolster.
3. Disconnect 5-P connector from under-dash fuse box and 7-P connector from main wire harness.
4. Remove steering column covers.
5. Insert key and turn it to "0".
6. Remove two screws from switch and replace.