Running Rough

I have a 1999 F-250 7.3 Diesel Crew Cab 4 x 4 Automatic. It has 467,000 miles on it and it runs like a top unless I let the fuel go below 1/4. When it ever gets down to 1/8 of a tank of fuel it acts like the engine is about to blow. It shakes vibrates and runs very bad. It actually makes you think that the engine has blown a piston or something. If I keep it over 1/4 it runs excellent. Has anyone experienced this with their truck? I thought I drained the fuel tank once and got rid of bad fuel but it must be something else.

Thanks