I'm also not convinced the guidance systems on the missiles are able to account for being fired from a moving target at mach 3.2 to hit something at 3.3 over at the very least 12,000 ft of altitude and whatever distance.

Not including acceleration because I've no idea how you'd add that.

The r-40 goes 5023.8 ft./s amazingly just shy of 1 mi/s (5280 ft.)

from wikipedia, its max range is 37mi and this assumes they don't have to give up any max speed for this, So that's 195360 ft.

sr-71 is 3684.1 ft/s at 80,000 ft which is 12,000 ft above a mig-25 at 3572.5 ft/s at 68,000ft.

Mach 1 = 1,116.4[3701] feet per second = [rounded off.]

R-40 is 5023.8ft/s that closes on the sr-71 at 1339.7 ft/s. It can do this for 38.88 seconds (max Range / top speed = flight time. 195360 / 5023.8 = 38.88)

1339.7 * 38.88 = 52,087.5 ft closer the r-40 can catch up by. If the mig 25 is within 50686 ft or 9.6mi or the SR-71 the R-40 has enough fuel to hit the blackbird. It's not 52087 as remember there's at best 12ft vertically is has to make up. Triangles and all that.

Bare in mind 2 planes chasing each other the sr-71 is 111.6 ft. further away every second.

Basically to catch one they have to keep a MIG in the air at ALL times and in interception range. I don't know how long it takes to get one to 68k ft. I was going to see if their radar gives them enough warning to get a mig to altitude but I guess they can monitor that from anywhere so I don't know really.

No I won't work out how far away they have to be head on. My guess is quite a lot. But if the SR-71 turns it can probably easily avoid the missile. They can tell if they've got radars looking at them so they know if there's a missile lock.