Well I don't know what you did there, but they are not completely right in saying 'they need to be re-calibrated to get the engine running'. It is recommended that you get the injectors balanced after doing a nozzle swap as the 'crack off' pressure of the injector can be out. What they do is shim the springs in the injector body until all for units fire off at the correct pressure. You must have had air in the pipe work and nozzles still, not to get the engine to fire at all. Don't forget your injector nozzles would have had no fuel in after to took them apart.
I had to keep 2 injector pipes loose at the injector ends and spin the engine over until I could see fuel running down the injector body. Once this had be done on on all the injectors I then tightened all connections and spun the engine over until it fired, which probabily took 4 or 5 goes.
Once the engine had started, it ran rough for a little bit until the fuel was all through and then it was fine.
I then used VAGCOM to decrease the injection quantity slightly to smooth out the idle a bit and so the engine does not smoke too much at this stage as I have not got it remapped yet: I am only using a boost controller at the moment which gives me a higher boost pressure of about 1.2 bar constant, which will cut down of the amount of smoke to some extent.