Might need to adjust the valves? or possibly check the injectors? it really shouldn't shake as you describe around 1000. are your engine mounts shot? i know mine are and am replacing them this winter with OEM mounts..did as he suggested and adjusted the idle to 950 RPM. The engine vibrated excessively, to the point the brackets on the heat exchanger broke. I readjusted the idle to 1250 RPM, and the engine idles smoothly, and shifts well, with no issues in 1,700 hours.
I think the fact that the M25-XPB is a three cylinder engine has something to do with the idle needing to be higher than other engines.