96 civic was overheating while idle, checked fuses, 20amp cooling fan was blown, replaced it and still the fan does not come on except when I turn the engine off and then only runs for 30 seconds before turning off, any ideas?
I have also swapped the cooling fan relay with one I know works and same result.

 

Possible air in the system. Bleed system and try again. Also try to manually jump the fan switch and see if the fan runs that way too (just to confirm).

 

^ jump the fan switch. Its a blue and a black wire close to your passenger side headlight. If you feel that it is good, swap out the fan switch. It is located on your thermostat housing.