I did a pump swap on my wifes 04 Cooper but we still have issues. After we did the pump i took a test drive and i worked for a couple blocks. I found that the 5 amp fuse was blown,replaced it and the second one blew as soon as we started the car which would seem to me to be a short in the harness some where. Would a bad fan kill the fuse or do i need to dig deeper?

 

yes a bad fan will blow the fuse, mine did the same thing.