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Hello and thanks for using JustAnswer!
I am Derek, an ASE master certified technician, and I will be happy to help you with your Ford Mustang.
What fuse keeps blowing? Can you give me the fuse number, and what fuse box is it located so I can look up more information about your vehicle.
What engine is in your Mustang?
If the theft system were a problem, it would not cause fuse 41 to blow. An anti-theft problem would cause a start and stall condition and a flashing security light on the dash. I do not suspect this is causing your concern.
Fuse 41 powers the fuel pump relay and fuel pump. If fuse 41 is still blowing after a new fuel pump it is highly likely you will need to replace the fuel pump driver module (FPDM)
The fuel pump driver module controls the fuel pump voltage, and this module can short out internally causing the intermittent problem you are experiencing. I would recommend replacing the FPDM. It is located in the spare tire storage compartment.
If you have any other questions please feel free to ask.