Humm... I probably would feel sick too... but then, stuff happens.

Not having to wake up to a flood or a fallen tree over the house caused by a storm, makes up for all the screw ups that
I made over the years...

Now, you said that the bike looked as if it had never been washed. Are you sure that the scratches weren't there all along? ???
I would start by washing all the affected areas with dish soap and water. Sometimes the residue of some compounds
will accentuate minor imperfections.

As you suggested, whatever Jim tries next, do it say, under and / or behind the pipes. If and when he finds a potential fix,
try it in a small area of the surfaces that need fixing.

Do not do this on Chromed-plastic. It'll probably peel right off.

At any rate, there is a product called BLUE-JOB. It is made to remove the Blue-ish stains off the Chrome Pipes.
Would it work on scratches? I don't think so, but further research might prove me wrong.
Otherwise, the main solution is to re-chrome.

However, if things are so bad that rubbing compound would not make it worse, I would gently try "Soft-Scrub" first,
applying it with the finest steel wool available.

Make sure that any steel wool is thinner / smoother than the applicator given to Jim by the P.O.
If Soft Scrub doesn't work I would then apply the rubbin' compound as a last resort.

Make sure that any product you use is applied in one direction, rather than using a circular motion.
Beware that some chrome pieces are not metal but plastic. If so, fixing those might be nearly impossible.
On those, the chrome might actually peel off.

I realize that what I do is not a solution to your dilemma... and painting definitely IS NOT for everyone...
I for one prefer Black over chrome. Given my preferences, I often use rattle-can Black Primer then, Satin-Black or Semi-Gloss paint.
Many mufflers would show a straight / linear scratch that cannot be buffed out. In such cases, I mask the outer edges of the scratch
along the entire muffler...
making sure that the "design" matches on both sides. I use High heat Engine Primer and Paint and spray the exposed areas to match.

I've gotten good enough at it that some observers ask how much did it cost me to powder coat.

Finally, it is likely that most damaged pieces could be purchased used but in good condition on eBay.
I certainly hope that you folks find an acceptable solution.
Good luck.
PS: I am at the early stages of negotiating a trade; my car for a low-miles VTX 1800.
"Life is what happens to you while you're busy making other plans."
John Lennon