If you REALLY want the ref, AFAIK, it is CFSM 3-13G-002. Special size personal allotment clothing, footwear and orthopaedic furniture, Para 5(a) to 5(d).
But, even IF I am correct, its not important. 8) First question is "why"; do you need special, or do you want special boots.
(1) If the reason is "because I like these gucci boots", as indicated you are SOL like Occam said.
(2) If you have a legitimate medical/fitting issue, you'll likely be sent to the foot clinic on base, assessed, and then that will go to Supply, who will kit you out with the approved 'special size' boots that will become your issued boots.
As SKT said, though, talk to your Div CofC; they'll get things rolling IF you fall into (2).
Not sure about Esq, but in Halifax (not sure what coast you're on) there used to be a foot clinic on the 1st and 3rd Wednesday of each month at 3rd Floor, CF H Svcs C (A) aka Stad Hospital. IIRC, time was 0900-1100, no appointments needed but you could make one anyways. That is the starting point for people in Hfx; Special Sizes on the dockyard couldn't do anything without the referral from the foot clinic. Now, that info is dated 2 years ago when I got my last set of orthodics and boots, so very likely has changed. All of which your CofC can find out or verify when you talk to them.
If your West, I have no idea how this works there.
If you have a legit medical / fitting issue with the standard boots, you should be able to get 'special size' issued ones.
:2c: