I couldn't find this mentioned earlier in the topic, so I'll mention it now.  The 300TDi automatics had a greater output than the manual varients, they were "tweaked" slightly already from the factory to make better use of the automatic gearbox.  With your engine having come from a manual vehicle, that means it will not be giving the same performance that another 300TDi auto would be.  Although we're only talking about 5-10bhp, but that can make all the difference I think.