Since your symptoms are entirely engine related, I highly doubt that the transmission is part of the problem. It is entirely possible that the "worst" is part of the equation here, but lets not jump to that conclusion right off the bat. There are far too many things that can cause the symptoms you have long before catastrophic failure.
As with all of my answers regarding Detroits, you need to start with the fuel system. Fuel systems seem to be the weakest link on Detroits, the slightest issues there can lead to the hardest to diagnose problems. Anytime you have a rough running, low power, and/or smoke issue on any big diesel engine, you need to start with the fuel system first and work from simplest to hardest in terms of diagnostics.
Begin with the fuel filter, something as simple as a clogged filter could cause the symptoms you describe. The new ULSD fuel is notorious for acting as a cleaning agent, removing years of sediment from fuel system components and clogging filters. Biodiesel has been known to cause the same problems. If you find that your fuel filter is clogged, be sure to carry a few spares with you because you will probably run through several filters before the system is clean enough to stop clogging them. Make sure you don't have a significant amount of sediment in the tanks or an algae problem.
Also check to make sure that air is not getting into the system somewhere. Check all fuel lines, fittings, and valves. Don't forget to check the anti-drain back valve, which when bad, will cause the engine to lose it's prime and therefore be hard-if not impossible-to start. Air in the fuel can be difficult to track down. You need to look over these components with a fine tooth comb, remembering that the hole may not be in a spot you can easily see, and there may be no leaking fuel at that point to help you track it down.
Have the fuel injectors tested, and the injector cups checked for wear. You should also have an overhead run (an adjustment of valve lash, engine brake etc.) Far too many owners neglect to have these adjustments done on a regular basis which can lead to a loss of power and fuel mileage over time, and eventually to rough running conditions.
After you have ruled out the above issues, move on to the air side of the fuel/air equation. Have the turbo impeller shaft checked for excessive play, make sure that the charge air cooler isn't leaking, and that the air intake hoses are not collapsed.
If the engine is throwing any codes your job is made a little simpler. You may be able to pinpoint the issue depending on the codes thrown. Either TRS or SRS (timing) sensor could be out of whack, effectively giving your engine the wrong information to run properly.
Based on your specs, (900L, Detroit, Auto Shift)I am guessing that this is an old company truck with out the "owner/operator" gauge package. You can purchase and install additional gauges to help keep yourself informed of how your engine is operating and to help you diagnose issues like this one. A fuel pressure gauge and pyrometer (exhaust temp) can be indispensable in determining the issue at hand by letting you know if there is a restriction in the fuel system, or if the engine is running leaner than usual.
Good luck.
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