Hello, rabies vaccines usually will cause a reaction much like what you saw in the first 48 to 72 hours after the shot. They will usually become lethargic and sore at the injection site but that will usually subside after a day or two. What he is going through now sounds rather extreme for a vaccine reaction. Have they run any blood work or taken any x-rays?
As far as getting the vaccine out of his system there is really not a way of doing it that I know of. You can give Dexamethasone injections and possibly some Benedryl injections to try and combat the effects of the shot but since it has been so long it would be hard to get anything out of the system. I would pump your vet for more information on your babies case. If he is not able to give you information on what is going on or does not want to give you information on his case then I would seek the help of a second opinion from a different vet. If you are afraid for your babies life and health then I would consider taking him for a second opinion if you are not comfortable with the vet you are at right now. Please be sure to let me know if you need anything else or have any other questions.