The good news and bad news is that you won't be transferring anywhere until you're qualified. Go to talk to your DH and your XO and explain what's going on. You're likely going to be on LIMDU and pulled from the ship for the duration of your recovery (crutches aren't compatible with sea duty), and that is going to seriously hamper your progress. While LIMDU, you're probably going to be stashed at DESRON/PHIBRON/LCSRON/etc. which could mean you have plenty of time to study and talk to SWOs of all backgrounds and brush up for your SWO board. The bad news is that you won't be able to demonstrate that knowledge to your CO which is going to hurt your progress. It's fucked up that your CO won't qualify anyone, that's bad for your careers and has long term effects. Now, here's the secret your CO, XO, and DH won't tell you: It looks really bad on them if there are multiple officers at the command who don't qualify on time or don't qualify period. If that happens, PERS-41 is going to be up his ass asking questions and both he and you will have to write letters to PERS to explain why. So he has incentive to get you qualified. First step, go talk to him. Second step, go under the knife and focus on getting healed up.
What are you planning on trying to redesignate to? If it's to another URL designator (Aviator, NFO, SEAL, etc.) you may have a tough road ahead. Depending upon how long your recovery and qualification process takes, you may be too senior to transfer into those communities. They want you to be able to have enough time to get through the training pipeline and then make the necessary career wickets before being screened for O4 and Department Head. Once you're healthy and close to qualifying, call the community manager and pick his brain:
http://www.public.navy.mil/bupers-npc/officer/communitymanagers/Pages/default.aspx.