90 civic dx 1.5L check engine light problems?

i have a 90 civic dx, my engine light comes on once the car is warmed up. i get 12 short blinks on the ECU and i believe that is a EGR valve. i replaced the EGR valve, egr solenoid and i have vacuum too but the engine light comes on when its warmed up. when i switch it off the cel is gone then comes back on after driving for a while. what could it be? need help please. Also i replaced the transmission and now the new transmission has hard shifting. help would be highly appreciated. thanks.