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I would start with putting a compression tester on it. Check each of your cylinders to see if the compression is within spec. If it isn't, than you probably have internal engine damage. Could be something as simple as a blown head gasket allowing your compression to escape into the cooling sysetem or crankcase, could be piston rings or a connecting rod. The thud doesn't sound like a backfire into the intake does it? You could have jumped timing.
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