So I just swapped the motor on my 98 honda civic with the exact same motor, d16y7. Yesterday the car was running perfectly fine, but today after starting it and letting it run for about 2 mins the car shut off and the main relay assembly starts clicking. I just noticed that i had left the gas cap off since yesterday. What can be the cause of this?

 

BUMP

 

well you kind of answered your own question... Do you have a check engine light on?? A gas cap is needed to help the fuel pump fully pressurize. Check the main relay also, they are notorious for going out in Hondas...

 

When I start the car there is no CEL on. However, when the car shuts off the main relay starts clicking and the CEL and D4 lights blink.
How would i check the relay?

 

bump for some much needed assistance

 

Problem solved!
Turns out i forgot to bolt down the thermostat housing ground and the gas cap was off!