Our '64 had clearcoat which we stripped. The failed parts weren't really "dark" they were oxidized which gave it more of a "dull" look. Once stripped, the protected parts were actually still shiney with the failed clearcoat areas looking grey & dull.
The dark portions, if really dark or black, could be a couple of different things:
1) do they look like "rub marks" from a cover or tiedowns? Usually this are somewhat linear...look kinda like skid marks
2) do they look like "burn marks" from a previous polishing attempt? Usually these are roundish dark gray, they can be shiny and can be best seen from an angle rather than straight on...they kinda look like ghost images
If #1 they can usually
be polished out using the technique at Perfect Polish
(or Vintage Trailer Supply - they are the same). Unless they have rubbed through the Alclad layer, then same as #2. If they are #2 this is where the purer aluminum Alclad layer has been worn through...this is not repairable unless the panel is replaced. Polishing will make them look better at first, but they return quickly.
If you can post pictures that would help us figure out what you have, or you can look at our website's polishing section to see the failed clearcoat dullness I'm talking about. We didn't have any of the #1 marks but we have one of the #2 marks on an access door (streetside)...but it doesn't photo well so I doubt you will see it.
Mosty people do not re-clearcoat their trailer after polishing, as that clearcoat is destined to fail too. There is maintenace involved with having a shiny trailer, it's not a one time thing...are you thinking you will be handling that or will be having someone else do that too? It could get cost prohibitive if you have to pay to maintain it over the years...
Good luck in wahtever you decide to do...feel free to ask questions, either online or via email/PM.