If you have a 9F/Xe/Y engine,
no vehicle or compliance plate
how can you tell if it was from a 69mk1/2
or a mk2 cooper S,
or a Leyland mini GT,

the three registers the numbers do not exactly run in ascending order

Post the engine number here or check the Cooper S list on here.

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DrMini- 1970 wasaMatic 1360, Mk1S crank, 86.6HP (ATW) =~125 @ crank, 45 Dellorto (38 chokes), RE282 sprint cam, 1.5 rockers, 11.0:1 C/R.

I realise you have the register

but the three vehicles I mentioned, do not appear to have the engine number stamped on compliance plates

Because the compliance plates don't show engine numbers the only way to know for sure is the Passports to service, purchase documents, or one owner cars.
They did jump around a lot but you should be able to work out the year.
51000 to 54000 could be 1969.
53000 to 56000 could be 1970.
55000 to 56000 could be 1971.

69 will often be a MK1 block with Mk2 numbers

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1970 Cooper S ex-Bathurst & ATCC
1964 Austin Cooper S ex-Group C race car
1967 Morris Cooper S ex-Group B
1962 Mini Speed sports sedan
1968-71 ex-Peter Manton Shell car