Need to know the difference with the 4 litre compared to the old 3.9 litre
what has to be changed over to make the 4.0 litre work in the EA?

It will depend on whether you've got a log manifold (ie Multi-point fuel injection) or CFI. If you just use the bare block, head & sump, all of the 3.9 parts should bolt on.

Here's a link that might be helpful.

ford-4l-and-6-cylinder-f1/about-the-different-ford-6-s-and-engine-retrofit-information-t31883.html