1995 mustang cobra svt, 5.0 auto/od OK I parked the car and let it set for one day. Prior to that the car was getting hard to start, it would start on the secound attempt . When I started it after it sat, it started and ran very rough, like it was not hitting on all cylinders ( it shook the car) So I decided to change the plugs wires and dist cap and rotor. After doing that it ran the same... so I changed the fuel filter. When I took it off, the fuel that came out of the filter looked like coffee.. so I decided to drop the tank and make sure it wasent rusted or very dirty. The tank was super clean... so I changed the pick up screen because I broke it while checking the fuel pump ( witch was very clean ) I drove the car a short distence thinking I might have gotten some bad gas or something , but no change... so now I plan on looking for a vac leak or anything you can tell me to get on the road... last night when I started it the check engine light came on ( did not flash ) So that's where I stand now... hope you can help me out... and I am not that knowledgeable about what or where oxygen sensors are so if you help I would learn a lot during this process thanks for taking the time to help.. rdn I have tried to do a self test to get the codes ,but no codes... thanks rdn

Replace the Mass Air Flow (MAF) Sensor. Stay away from remanufactured MAF Sensors, since my experience has been awful, and go with a new Motorcraft part. Afterwards, clean the air box and replace the air filter (pleated only). Stay away from oil impregnated (K&N) air filters--the oil from them ruins MAF Sensors.

I think you were on the right track by pursuing the "coffee" you found in your fuel filter. I can assume that you meant from the fuel tank side of the filter? Since the tank was "super clean" you will need to search elsewhere for the problem: rusty fuel lines.
Start by testing fuel pressure while the car is running poorly. Don't replace any more parts until you find something that has failed.
Retest for any diagnostic codes and let us know.