PaulS:
That method of counting pulses absolutely guarantees that you will miss pulses.You have interrupts turned off most of the time. Yet, you expect to send and receive serial data with interrupts disabled. That is NOT going to happen.
count1 is incremented by the ISR, and used by loop(). Yet, it is not declared volatile, so loop() has no idea that the variable was updated by other code.
Leave interrupts on ALL the time, except for the VERY brief time you make a copy of count1 and reset it to 0.
So you are saying to do something like this in the main loop:
recvInfo();
lightLED(); //Function for motors
ultrasonicSensor(); //Geist sensor function
ultrasonicSensor1(); //Quarry sensor function
noInterrupts(); //Disable Interrupts
count1 = 0; //count variable for flow meters
interrupts(); //Enable Interrupts
flowRate = (count1 * 2.25); //Take pulses and multiply by 2.25mL
flowRate = flowRate * 60; //Convert seconds to minutes
flowRate = flowRate / 1000; //Convert mL to Liters (L / Min)
Serial.println(flowRate); //Print flowRate to Serial
Serial.flush();
}//end loop