Engine runs rough in 2005 tdci can't find the problem, got the chance of a cheap running engine from a 2003 with less miles on, only difference appears to be turbo is electronic on our 2005 and vacuum on the 2003 replacement engine, will that be an issue or is there any other down sides or problems?

The 2005 is Euro4 and the 2003 Euro3, on the Euro4 the ECU controls the electronic actuator the EGR is a different design as well

the way to do it is to get the engine, ancilliaries, ECU BCU, all locks and keys off the 2003/Euro3 engine

Alternatively, you could use the 2003/Euro3 base engine (block/head etc) but with the 2005 /Euro4 turbo/actuator/EGR/ECU BCU/locks keys - BUT - if the fault lies in the turbo/ actuator or other parts you are still using, you have wasted your time

one way the ECU/BCU "thinks" its the 2003, the other way its the 2005, if you follow. - some of these components cannot be mixed, without an expensive dealer reset, if at all - there may be other problems, like the pick-up for the speedo, and a 5-speed/ 6 speed gearbox issues, if you have heated seats, the seat loom is different etc (pre/ post facelift) - it could be a whole lot of hassle - depends on your resources/ ability/ experiience etc