Hi I've put an engine in my fabia 1.9 sdi 2003 an obviously the pump is immobilized so I swapped the top half the pump and it kicked in for about a minute filled the garage with smoke and then cut out since then it won't fire. When I crack the injector pipe their is loads of diesel out of 2 and 3 too much in fact but nothing out of 1and 4

Does it require some sort of timing??????

you need vagcom to introduce the new pump to the old ecu, or swap the pump over from the old engine.

why did you change the engine?