Looking very strange to me is connecting the serial output of your GPS receiver to pin 2 but the signal of your flow meter to pin 1. If you use pin 2 or 3 for the flow meter you'll be able to use an interrupt to count the ticks of the flow meter.
Any of the 6 analog inputs of a standard Arduino can be also a digital input or a digital output.
For the GPS unit you probably need a level converter (a logic HIGH of 2.4 V is not enough for a 5V Arduino).