I think you would have noticed if rain water had got into the cylinders when you turned it over to start it,before you do anything else pull the dipstick and see if the oil level has got higher,if it has it probably has water in the oil but by what you explain sounds more like there might be water in the fuel,drain the sediment from the tank,turn off the fuel supply valve and remove the glass bowl,rubber gasket and flat filter gauze above it,turn on the fuel to check the flow,clean the gauze filter and bowl and put them back on turn the fuel on and loosen the bleeder on top of the filter,the fuel should gravity to there,on top of the injector pump is a tee,remove the two pipes attached to it and then the tee,there should be a decent flow of fuel at that point,it helps to have the tank filled,blow out the tee piece and put it and the lines back,start the engine.keep the revs below 1000,if it does not smooth out in a minute,turn it off and have someone have a look at it for you.
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