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I would've guessed lean condition in cylinder. Maybe head gasket or cracked head?... If timing was out both cylinders would be hot. No matter, if it's knocking pretty bad, you'll be tearing it down.
My first guest for one cylinder running lean would be an intake manifold seal leaking.
With the rear pipe heating up I'd check over tightened exhaust push rod or valve seat not sealing.
Knocking just plain isn't good.
I'd start with a compression test.
 
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