Yes, it's a good idea to let the threads soak in penetrant for a while, but not so long that it dries out. I believe penetrant is formulated with a mild acid. Once it does its job it should be cleaned.
Ditto on PB Blaster (also Kroil).
Definitely put a light coating of antisieze on the threads before installation.
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95 E320 Cabriolet, 159K
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