I asked TfL about this and they only care about the classification of the engine, ie is it Euro 4 or not. They don't test for emissions.

DVLA only require a receipt for the engine or confirmation from the garage that the engine was swapped. They don't require a test for emissions.
https://www.gov.uk/change-vehicle-de...idence-to-give

MOTs from what I can gather test for emissions against the oldest componant of the two, ie a 2005 engine in a 1995 car will be checked that it passes the emissions test of a 1995 engine.

Or have I missed something?

I understand an engine swap might not be straightforward. That's why I'm asking here.
Has anyone put or seen a Euro 4 or 5 engine in a 90s car (not necessarily for ULEZ reasons) so I can see what's involved?