If some Thresher/Permit class boats were launched with red anti-fouling from the waterline down, this would have been definitely a shipyard paint job. Standard Navy scheme would have been red anti-fouling from mid-axis of hull down, and black or a very dark gray (virtually black) from the mid-axis upward. At the Vallejo Museum where two of my 1/96 scale static models are, one of Permit in the Navy scheme, and one of Scamp as launched with red from the waterline down in shipyard painted hull colors.
Paint your Thresher/Permit with the black/red separation at mid-axis. The only other variation at all possible was that the Navy was experimenting with a new anti-fouling paint in the late 1950's into the early to late 1960s, called 'Mare Island anti-fouling black' or just 'Mare Island black'. Mare Island NSY had a paint shop Laboratory for the Navy to experiment and test various hull preservative coatings. Albacore ( hull painted all black is such an example. Thresher at the time of her loss might have also been painted in this scheme, but I cannot confirm this definitively yet. I have a color image of Barb in dry-dock showing her prop clearly and Barb's 'puff' arrays on her horizontal stern planes (ala Sturgeon 637 and Barbel 580 class boats). Barb was the trials boat for these arrays, and was the only Permit class boat configured with them. It is not real clear in this color image (some what washed out color) but the entire boat appears to be painted all black at that moment the image was photographed (my guess circa 1967?). Unable to post photo here, just email me and I can send it to you then.