midiean:
I was able to figure out the issue. researched and found that I needed to be using a modulus to determine if timer/100 had a remainder of 0 to auto-increment pumpClock.
Ah. That is what you attempted by ...
if (timer/1000){
. . .
}
You wanted ...
if ((timer/1000)*1000 == timer ){
. . .
}
Or
if (timer%1000 == 0){
. . .
}