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Recheck the timing on the timing chain.
If the valves, seats and guides are good and the piston rings are good. I suspect the timing is not correct. I have a 2011 Cooper S and replaced the timing chain. Using the engine timing tool you must remove and replace with a new crankshaft sprocket bolt and perhaps at least one of the VANOS camshaft sprocket bolt to get the chain to set the aliment of all three sprockets. I don't see how you can get the chain to go back to its original positions on the sprockets precisely. Low compression suggests valves are closing late on the compression stroke thus not getting full compression, if the valves and rings are good.
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