2. I set it for mach 3 as that's roughly how fast the SR-71 is flying.

It flies Mach 3, but you are setting radial speed, so it should be bit lower.

5. The reason I only use 1 missile for this engagement is simple; no US aircraft has ever been fired on by an S-200 before. Therefore, the SR-71 will never even know it's been engaged and thus won't be maneuvering/evading. Of course in real life I'm sure the CO would've ordered 3 missiles fired.

SR71 was a high prized target, so I bet than in a case of receiving firing order, a battery would launch all missiles possible.
(more than 6)

5. The reason I only use 1 missile for this engagement is simple; no US aircraft has ever been fired on by an S-200 before. Therefore, the SR-71 will never even know it's been engaged and thus won't be maneuvering/evading

Launching a Vega missile is not detectable by RWR's.
The only time US NAVY faced the Libyan S-200, they sent forward the Ticonderoga ships to detect the huge missile while flying.
(they did it successfully)