exactly. just jumping into boot camp is not enough to bring you back to 100 percent. It may even hurt the recovery process. if you are 100 percent certain you want to go into it, i would suggest giving yourself a time table and plenty of time between now and when you enlist. this way you can gradually work out, weight train etc, so it wont be such a shock to your body and you will have built the muscle back.
i dont know the extent of your procedures, but if they are what i got out of your explanation i would get a good 10-12 months of training so you dont hurt yourself