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this sounds like the engine may be misfiring?
if the issue is only when moving off from a standstill then yes it could be a transmission fault ( as you've pretty much replaced everything else)
what state was the gearbox oil in?
if it was really dark and sticky then you may have try dropping the sump pan off the unit so you can also wash out the filter screen inside as if its clogged up this lowers the internal oil pressure and makes the transmission slow to shift and malfunction
however if the fault is there whenever you accelerate I'm inclined to think its engine related ?
so I'd suggest o replace the fuel filter and also check that the EGR valve isn't stuck open and clean it out if it is