Mustang06v6

I’m new to this but I’ve tried so many things and not really getting anywhere so hoping I can get some help! I have a 2006 v6 coupe. Over the weekend we put in a new battery, new smart junction box, keys programmed. Started no issues ran all weekend. Monday morning go to start the car and she wouldn’t start only crank. I sprayed some starter fluid and she started right up, I drove about 42 miles that day where I had to turn the car off a few times and she started right up every time. That evening after I’m home car was sitting for about 45 mins maybe an hour I go to start it and it wouldn’t start... tried the starter fluid again cranked and turned over and then shut off after a min running... started again and then once I went to go rev after it was idling for 5 mins it shut off once I touched the gas pedal... tried the starter fluid and got nothing only cranking and not turning over. We have replaced the spark plugs put new fuel filter tried to scan for codes and I’m getting no where it will only crank and not turn over... we do hear the fuel pump when we put the key into an on position but not smelling gas under the hood. To also note when changing the fuel filter when disconnecting gas didn’t just shoot out (which I thought it would from the line) and what we saw come out of the old one was a brown color like the gas is dirty...