Hi David.
I would say that if you keep the V5 up to date, there should not be a problem.
It is easy to check the engine number against the cars vin plate. Ford use the the engine number as the last part of the VIN.
If the engine number is still legible you can check at a glance if the car has its original engine.
My advice, Buy a suitable car, wait for DVLA to send you the V5. Once you have it, send it back to DVLA to notify them of the new engine mumber.
This will keep the cars records up to date. Keep the car on SORN until you are ready to register your build.
DVLA will normally only question an engine change if the taxation class is affected or the type of fuel has changed.
Burton power have a usefull guide to Ford engine production dates.
Linky