The impulse counter is not supposed to be connected in series with the pump. If you do that, there will be no (or very little) voltage across the pump. You need to leave the pump connected as it was before.
So the counter uses a contact closure to tell when to increment its count. Is there any way to change it so that it will increment its count when a voltage is applied? If so, do that and connect it in parallel with the pump. Each time the pump runs, the counter will see voltage and will increment.
If the counter only accepts a contact closure, you can use a relay to produce a contact closure when the pump is running. Connect the relay's coil in parallel with the pump, so the relay activates while the pump is running, and connect the normally open contact of the relay to the counter. You can use any relay with a 12V DC coil and at least a single normally open contact (SPNO). You can use a relay with a changeover contact (SPCO or SPDT) or two changeover contacts (DPCO or DPDT) as well; just use one normally open contact and the "common" contact.
Radio Shack have some overpriced NTE relays such as
http://www.radioshack.com/nte-r22-1d16-12-relay-16a-dc-12v/55077108.html but I guess you want a good quality one with a mounting tab for convenience, right? Have a look at
http://www.digikey.com/product-detail/en/1432772-1/PB685-ND/807762