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Do you still have the old intake manifold that you replaced?
Did the intake runner shaft have a ton of play in it? Is it possible that the bushing from the intake runner shaft wore out and dropped inside the engine? I have seen that before. You might have to cut the old intake apart to see the old bushing.
Please let me know if you need additional information.
Ok. It must have been really bad to make an injector knock. They typically don't get that noisy.
Please let me know if you need any help in the future.