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When I was taught to drive stick, I was taught to leave it in gear while slowing down. The engine compression would slow the vehicle and it would save wear on the brakes as well as prevent the brakes from overheating.
Given that my truck is pretty heavy, I like to keep brake temps low.
Fuel cut will also reduce or stop all together the feed to the injectors and this will reduce fuel consumption... An added bonus in todays high fuel prices.
So I do this, but it gets a bit uncomfortable in the F350 because when I let off the throttle, especially at high speeds and especially with heavy loads, the truck bucks like I'm pumping the throttle.
Umm my 1993 F250 doesnt do that, i almost always leave it in gear while slowing down. Ill pull it out of gear at the last second before i stop usually around 1000RPM.
It sounds like there might be a problem with your truck.
I use Diesel Kleen in my fuel on a regular basis.
Keeps everythig clean and lubricated.
With a problem like yours, I would change the fuel filter, fill it with Diesel Kleen before you install it.
Then dump the rest in the tank.
When you start the engine it will run a bit funny for a minute or so, but the strong dose should start breaking up an crud.
You should be back to normal (no surging) before the tank is empty.