1998 Mustang V6 engine knocks and runs rough

I have a 98 v6 mustang that ran great and all of a sudden, it wouldnt start. so, i used starting fluid and it started. It ran fine, I let it run for an hour or so, took it for a spin, and when accelerating, it made a little knocking noise. So, I parked it, and the next few times I tried to start it, it wouldnt start. When I finally did get it started, it knocks really badly,runs rough and wont stay running for more than a few seconds. I had it towed to a shop, they said the fuel pump was bad. I relapced the fuel pump and the problem persists. The fuel rails are full of fuel too. Any ideas?

Did you ever loose oil pressure?
Roll it over by hand to TDC tell use where the rotor button is located.
Did it over heat prior to this happening?

Could have spun a bearing. Sounds to me that the problem lies internally inside the motor. Also, I've had bad experience with starting fluid..