His Baseball Reference major league page doesn't mention how he got to head to AAA San Francisco (Boston system) and then Miami later in his career, but we can fill in a couple holes.
From the Miami (OK) Daily News-Record of May 14, 1957...
"The Giants reached the 25-player limit by dumping four men and purchasing right - handed pitcher Stu Miller from Minneapolis in the American Association. Southpaw John (Windy) McCall was sold to San Francisco of the Pacific Coast League...."
The last Seals team was glad to have him, but he didn't have a good enough record for them and he was sent to Miami.
“That long-sought lefthander, John (Windy) McCall, was purchased from the Boston Red Sox today by the Miami Marlins for a price that would lift the bonded debt of a fair-sized banana republic.”
Miami was with the Phillies at that time. McCall pitched well enough for the Phillies to invite him to 1958 spring training, but he was optioned back to Miami before the season started.
McCall was with Miami in 1959, in the Orioles organization, and Seattle in the Reds organization. Haven't found the deal there yet.