Had the same issue you are having....
I dealt with a rough running 1994 4.9 for a year. I replaced everything you mentioned above. It turned out it was the fuel pump. My mechanic replaced it and then it went bad again (never buy Standard Motor Products fuel pumps, they were bad luck for me). Finally, on the third try, we went with a Motorcraft Fuel Pump and problem solved.
If you can, I would check your fuel pressure and see if it is consistent. It might be a good idea to replace the fuel pressure regulator, too. Fixing those two things worked for me.
Let us know what you find out.