You are pointing in the right direction but all this code does is to lose whatever number was in count1 by setting the value back to zero
noInterrupts(); //Disable Interrupts
count1 = 0; //count variable for flow meters
interrupts(); //Enable Interrupts
You need something like
noInterrupts(); //Disable Interrupts
latestCount1 = count1;
count1 = 0; //count variable for flow meters
interrupts(); //Enable Interrupts
...R