I don't think your fuel filters are the problem, but could be making your problem worse. Usually with the fuel filter starting to get clogged you will notice a loss of power, but will otherwise seems to run okay. It,s possible that old diesel could maybe the problem, but it would have to be pretty bad. Usually air in the fuel system will cause stumbling. It seems like you might have a micro-leak. A micro-leak is a leak which is too small to let fluid out of the line, but large enough to allow air to enter the line. If the fuel filter is partially plugged and you replace it, and it seems to run better or runs like it should then I would suspect a micro-leak between the fuel filter and the injection pump.I would start off by cracking any fuel connections loose then re-tighten them. Then check the lines. The next place I would check is between the inlet of the fuel pump back to the tank, lines and fittings. An air leak in the fuel system could happen anywhere along the line. I have run across leaks like this and it's on the suction side of a pump and usually a rubber line. Cut open your old fuel filters and check to see what's inside, if it's algae in the fuel you should be able to see it. It would look like a dark slime. If it is algae it must be cleaned out of the tank and lines thoroughly then add clean diesel and a biocide back in. I am not sure if the electric fuel pump has a screen on the inlet side or not, might be worthwhile to check it out. As far as the fuel cleaner, I'm not really sure what you really mean. I just purchase some FPPF Fuel Power from amazon and am going to try it in my diesel mower and diesel yard cart. Both seem to take a lot of time on the glow plugs for a cold start. If it helps, I will be impressed. Supposed to clean injectors. Looks impressive from the advertisement, but it's an advertisement.