A couple of years ago I picked up a new set of K1 rods from a local machine shop after I left them there to be used for some mock-up work. What I hadn't realized until a LONG time after is that the shop ran them all through the parts washer before I picked them back up, but didn't appear to have re-sprayed them with any type of corrosion inhibitor. So, when I FINALLY got around to taking them back out of the box, what I found was a set of eight "new" rods that had developed surface corrosion on both the rod bodies and the ARP 2000 bolts.

What I've done since is treated a couple of the rods & bolt sets w/ an Eastwood product that's supposed to dissolve iron oxide and leave a zinc phosphate coating. Yeah, the parts definitely look darker (coated) after letting them soak in it. The rod bearing bores clean up OK, but the other parts of the bodies still have surface blemishes even where I've used a ScotchBrite pad.

The bolts are the most suspect in my mind after having done some research on how corrosion on bolts can lead to eventual failure. Although they appear to clean up OK after the dip & ScotchBrite treatment, I'm concerned that may simply be masking where the flaws are from normal visual inspection.

Given what I've described above, would you think the entire set of rods are now questionable for performance usage, or the bodies should be OK as long as I buy new bolts?

I would have them shot peened. That process is used to strengthen rods anyway, so it can't hurt them. And if would restore the surface and remove any residue from the rust and chemical.

The bolts are paperweights. The rods should be shot peened to remove any stress risers.
Surface rust should not affect the internal structure or properties of the metal , so get a finish you're happy with and run them.

As said above toss out the bolts. You may consider glass beading the rust off the rods and caps, as opposed to having them shot peened.

help me learn...

if the corrosion on the rods is only on the surface, and does not affect the structural properties of the metal and can be cleaned off and used, why does the same surface corrosion on the bolts make them junk?

Corrosion on the shaft of the bolt that leaves a surface irregularity is a possible source of a stress riser that could result in failure after the part is torqued / stretched and put into service.

You are misinterpreting what ARP says.
Yes, some materials are susceptible to stress corrosion cracking. That's bad.

However, nearly all failures start at the outermost fiber. Any kind of surface irregularity can act as a starter point for failure. They're commonly called stress risers, although they might better be called stress magnifiers. The rod bolt is the most highly stressed part of the rod. Using one with pits or other problems such as dents might cause that rod bolt to fail in service, which is also bad.

On the rod body there's usually enough material to polish out the problem, or shotpeening if done properly can help.

R.