will later p38 engine work in old one?

will the later 2001 4.6 engine in a p38 fit and work in a 1997 4.6

I am sure it will.

Block might but think the injection system had changed, you would need its ecu and harness to convert or use excsisting heads and manifolds and just use a new block?

The stripped engine is the same except for the camshaft sprocket.

I have recently changed my 4.0 engine from a 1997 one to a brand new 4.0 in my P38.
There are slight changes:
The sump is different, the new one is aluminium but fits and is perfecly ok to use.
The Camshaft sproket is different so you need to use your old one, ideally a new one from the older engine design.
The Crank sensor is different again use your old one.
Apart from that no difference, I fitted it myself with a bit of swearing etc!I used the injection system from my old engine and did not change the ECU. It started first time and runs really well.
Hope this helps