Bad fuel can certainly make it run like crap, and a plugged fuel filter could easily be a source of problems too.

Before proceeding to drain the entire tank, why not do a little "IV bottle" experiment instead?

The fuel line from the tank connects to the fuel head on the side closest to the engine. Disconnect this side, and push the hose off the nipple and out of the way. Unless you have an in-tank or external lift pump that you installed, you shouldn't need to do anything more to that hose for the moment.

Now, replace the filter, and pre-fill it with clean fresh diesel fuel from a high-volume station. Take a long length of appropriate size hose (I believe it is 3/8") and connect it to the fuel manager head, and put the other end into your jug of clean diesel.

NOW start your engine and let it idle. Does the sound change within a few seconds of starting, smoothing out? Rev it a few times - smooth? If there are any mechanical noises / banging / tapping (listen to my video again)... STOP THE ENGINE AND FORGET IT - the problem won't be fuel related, and you are risking your entire engine.

If, however, the engine sounds smooth and correct... Then you might just have a batch of dodgy fuel! Yay for easy solutions!

Remember that loose line from the tank that is just sitting on the side there? Connect a cheap-o Mr. Gasket fuel pump to that, your long length of hose to the outlet... And put the other end into an empty fuel jug. Wire the pump directly to the battery that is conveniently nearby, and watch your tank pump ITSELF out. This is the fastest way to drain the tank, there is an anti-siphon device at the bottom of the fuel neck which makes sucking it out from there impossible.

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