Think I am finally getting to the bottom of this.
First to eliminate a few things:
1. Clutch cable has not been changed. Was working fine before the engine swap, so I know it's correct.
2. Clutch arm can only go in one position - photo below shows there is a master spline, and also the bolt can only fit in one place.

3. If the clutch arm is pushed fully forwards, so the release bearing is fully retracted towards the gearbox, the fork that moves the release bearing will contact the gearbox casing. If the gearbox, clutch arm and fork are all the same then the arm should always stop in the same position. I measured the distance between the cable fitting on the arm, and the cable outer mounting on the gearbox casing, and got the same result for both old and new gearboxes. Think this eliminates a bent / different clutch fork.
Then I remembered I had taken a photo of the escort flywheel before fitting. Just taken a photo of the original fiesta flywheel to compare, and they are different.
Newly skimmed escort flywheel:

Original fiesta flywheel:

Photos only really show that the centre is different, and don't prove that the thickness is different, but it seems the most likely explanation.
Looks like the gearbox will be coming out again at the weekend, and I will measure the flywheels...