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If you bought a body and/or any bare sheet metal, leaving it sit unprotected over an extended period of time was an invitation for trouble.
There are several "rust transformers", metal prep's, on the market which you should have sprayed on the bare metal to protect it.
Do not grind and/or sandblast the metal to get rid of the "stuff" that is on the metal, take it to a stripper, have the body dipped to remove the primer, etc., that you have applied to the body. After the body has been chemically stripped have it dipped into a neutralizing solution, which most of the strip shops offer. The metal will be a light grey in color after it it neutralized, it can sit for years in this condition with no rust and/or other issues occurring.
My 39 conv sat in an open field in Montana for 38 years prior to me finding it in 1996. I had the body dipped to remove the paint and rust. It came out of the tank as "white metal" with some panels looking like cheese cloth.
The company that dipped the body did not offer a metal prep/neutralizer as part of their service. I went to the paint store, purchased "JASCO PREP & PRIME" surface prep. which is basically phosphoric acid with some other additives.
I sprayed the bare metal using a hand pump spray bottle and put the car into a container for two years.
I would advise against the use of any of the Old School brews like vinegar, muratic acid, etc.