My 1995 F250 isn't quite running right. I had a bad gasket on a new fuel bowl lid I got, which caused some vibration (1100 to 1900 rpms) with some random pinging noises that progressed to a slight knock that you could only hear standing behind the front wheels. Ran it maybe 500 miles on the bad gasket and the vibration continually got worse until the knock started and I parked it. Replaced the fuel filter, lid, and gasket and it's running a lot better, but still has a slight vibration at idle and around 1500 rpms. Filled the filter bowl with ATF prior to installing new filter, as I usually do. If I rev it up, then let it down, it idles smoother for maybe a minute then back to the vibration. There was some gritty black stuff in the filter bowl when I changed the filter. Would a blown pickup screen cause something like this? Or is it just bad fuel? Or do i need to just keep running it to get the air out of the lines?

Took it for a test drive after changing filter, and it's VERY responsive to the throttle and runs really well except for right after it shifts, especially at 35 mph. It gets boggy sounding and rough for just a split second after the shift. All in all, it just isn't running right, but it's super responsive and ready to go except at the 35 mph shift.

Also recently changed the glow plugs and checked to make sure injectors weren't loose. None were loose. Under valve cover harness appears to be in good condition (no melting at plug or any other indication of trouble) and all the injector wires are snug.

Any tips on what to check next?

 

You said you noticed black junk in the fuel bowl. Check the screen to the regulator and clean it. Also i wouldn’t fill the bowl with ATF. Fill it with diesel or not at all. The pump is designed to fill the bowl after a few cranks you don’t need to fill anything

 

Couple things..
I believe you have the 4R100 transmission, if so.... the torque converter locks up at about 35 mph in 3rd gear depending on your right foot, then shifts into 4th at about 43 mph. Depending on your foot you may be right on the edge and the converter is trying to figure out what to do. (Speculation on that)

Have you pulled codes recently? Even without the check light you still may have codes.

Thoughts on the fuel...
What is your fuel pressure, do you have a method to measure?
What size is the grit, is it crunchy, soft like disolving plastic, chunky, slimy?
Does it look like it may be bio growth?

When you changed the fuel filter I am going out on a limb and assuming you kept the drain open and flushed all the junk out. I flush my housing with cleaner, rinse two stroke oil, wipe out, then put a good dose of fuel and two stroke in the housing prior to filter replacement then prime as required with a few key cycles.

Have you thought about doing a tank treatment for boi growth? I like the Clear Diesel and Bio Kleen from Power Service. I use a dose of Clear Diesel every three months as normal maintenance to the tank. Every fill up either gray or white bottle as regular treatment for the fuel. Bio Kleen is for when you know you have a problem, Clear Diesel is for keeping it clean.

You could just be picking up junk from the bottom of the tank from years of junk in the fuel and regular contamination. Have you done or do you know if the tank has had the Hutch/ Harpoon mod? If not it may be time to go in and clean the tank and do some upgrades.

 

the auto transmission in these trucks is the E4OD