Can computer issues cause fuel pump whining?

I have a 1997 Explorer, 4.0 SOHC. I had to replace the crank sensor; in doing so I disconnected the battery. It was disconnected for 2 or 3 hours. I've never had a car with a computer before so I thought nothing of both battery cables resting on the same piece of metal.
The Explorer now starts but it runs very badly. It won't respond to sudden acceleration and does not like to exceed about 2500 to 3000 rpm. All of this I figured was my lack of computer savvy with the battery cables.
The confusion comes in with the fuel pump (now 6 months old), which is whining quite loudly after only a couple minutes of run time. There was no pump whine before the crank sensor went out, (it worked perfectly and quietly till that time); the only thing that was done is the sensor change and I know realize the computer was evidently cleared by the battery cable incident.
Most importantly what might I do to get back up and running again I don't have enough to just dump it at the shop, and have'em call me with the bill.

thank you