so after hitting my old 1.9 tdi pd 100 atd engine of a drain

it ran dry and then knakerd the bottom end of the engine.
i sourced a pd130 asz engine and we got all that in and running, the first problem i have is really bad on cold starts, lots of white smoke and really lumpy for about 5-10 mins once it has warmed up it then runs ok. thats one problem! the next is i still have the ecu from the pd100 in, when driving it still boosts fine but its no where near as fast as it should be then once climbing up hills or driving on the motorway it goes straight into limp mode, i think this is to do with the ecu but im not posotive.
i have changed all the temprature sensors, new sidemount intercooler with 57mm pipes all round, injector loom.
i am toatally stuck on what to do, if i buy a new ecu ill have to get it coded to the keys wont i?
somebody please help me!!!
sick of all the problems,
thanks gino