Hello Adrian,
Personally, I wouldn't change it.
A syou have stated yourself a '66 car is now a fairly rare item which carries a certain amount of rarity value.... if you were to remove what is a major element of the car's orignality then you would also be removing a considerable part of it's value. It would also cost more to replace all the components than simply repairing the existing system.
You have another car to act as donor ... but there were a series of changes introduced between 1966 and '79 which would affect what might appear to be a strightforward swap. None of them are major .... but they all add up to a significant move away from the originality of the '66 car.
I would rebuild it to original spec..... I could imagine that if you didn't you'd soon begin to think ..."if only...."
The hydrolastic system is actually quite easy to rebuild and I actually prefer it for general road use ...mind you, I have the Churchill pump unit sitting in the garage which I bought when I had my 3rd mini back in 1972... so it's easy for me to say so... ;-)
Seriously though... I'd rebuild it to original spec .... there are too few original cars left these days.
Ian