I've fixed a car with the same symptoms by replacing the rack.
Take my theory with a grain of salt, but I thought the clunk might be, at least in part, due to "getting over the hump" in the steering shaft u joints, because the angles don't cancel each other out like a well aligned driveshaft does. Then because you don't have assist, you're putting more torque through the column and steering shaft than you normally would.
But yea I was sure to check turning each knuckle turning back and fourth once the tie rods were off, being such an odd problem
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