2004 D0FA swap into 2000 Mk6 D4FA — kept original ECU + VP44

[Kiwicamper]

Hoping someone's seen this combination before. Based in NZ, for context.

Background: original 2000 2.4L Duratorq D4FA (120 PS) had ~277,000 km on it when it threw a big end bearing in December. Got a second-hand 2004 D0FA (125 PS) installed as a replacement — told it has roughly similar km on it. Done about 800 km on the new engine since the swap. No oil or water leaks visible.

Key detail: we kept the original ECU and VP44 fuel pump from the D4FA and ran them on the D0FA.

Both pumps are the same VP44 family across these engines, and both engines are TDDi 2.4s, so it seemed reasonable at the time. Water pump (new last year) and radiator (new 3 years ago) also moved over from the original engine. The mechanic said he moved the turbo from the original engine across as well, though I'm not 100% sure on that. Old engine had a dual mass flywheel / dual clutch setup, new one is single.

Two issues since the swap:
Overheating under sustained load.
Foot to the floor up a steep hill, temp gauge climbs toward the red within about 2 minutes. Back off the throttle and it recovers within a minute. Cruising and light load — sits at normal temp.

Down on power, ~10–15%.
The old D4FA had a noticeable surge after 2k rpm — that's gone. Pulls okay but feels flatter throughout.

Has anyone run a D4FA ECU + VP44 on a D0FA (or vice versa), and seen anything like this? Any tests you'd suggest I run to help narrow it down?
Cheers.