No. Shelby Mustangs are not considered “stock” Mustangs. They are high-performance variants that started as (or were based on) Ford Mustangs and received significant modifications by Carroll Shelby / Shelby American (or, in later years, by Ford in collaboration with Shelby).
Historical context

1965–1966 GT350s: Ford shipped specially prepared Mustangs (mostly K-code 289 Hi-Po fastbacks from the San Jose plant, often in Wimbledon White) to Shelby American. Shelby then performed the real work—engine upgrades (Holley carb, high-rise intake, headers, etc., raising output to ~306 hp), suspension and chassis changes, brakes, fiberglass hood, weight reduction, stripes, badges, and other hardware. These were purpose-built to be more race-oriented than a regular Mustang.
Later 1960s models (GT500, etc.): Similar process, with bigger engines (e.g., 428) and further body/styling changes. By the late 1960s some production shifted more toward Ford, but they remained distinct from base Mustangs.
Modern era: Some (like certain Ford-built GT500s or GT350s) were factory performance models using the Shelby name under license. Others are “post-title” conversions—stock Mustangs sent to Shelby American (or authorized shops) for superchargers, suspension, body kits, exhaust, wheels, and other upgrades after the car already has a title.

In short, the defining characteristic of a Shelby Mustang is that it is not a regular production Mustang; the Shelby treatment is what makes it a Shelby.
What “stock” usually means
In automotive and collector contexts:

A stock Mustang is one that remains as it left the Ford factory (or with only period-correct, reversible options).
A stock Shelby means a genuine Shelby that retains its original Shelby-era equipment and configuration, without later owner-added aftermarket parts. Originality is highly valued (and heavily scrutinized for authenticity because replicas and clones exist).

Collectors, historians, and auction houses treat authentic Shelbys as their own category of high-value specialty cars precisely because of those modifications and the Shelby pedigree. Calling them “stock” would erase the very thing that defines them.
So while a well-preserved original Shelby can be described as “stock for a Shelby,” it is never considered a stock Mustang.