Any Pontiac guys on here? Need insight.

The scruffy intermediate shaft is common for an original shaft. The noise? Maybe it's not the engine, maybe it's the transmission and just transferring the noise up.
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Even though you just burst my bubble...lol..I want to thank you for that tid bit of info on the scoring on the pump drive rod. I'm sure it's motor related. I worked in a trans shop for several years in my younger days and I believe it's not coming from the trans.