In answer to your question, the "quarantine" or separation is because he needs to be separated from his dam until she dries up. Even after actual weaning, some foals will nurse for comfort, and if they do the mare will keep lactating or restart if she is not quite dried up. If you put them back together too soon, you will likely end up having to start the process all over again. It takes about 2 weeks for a foal to be actually weaned, but you should wait an additional 2 weeks before putting them back together. Those are just general guidelines, of course - both mares and foals will vary.
As Speed Racer said, the vaccs have nothing to do with weaning. The immunity provided by the colostrum only lasts so long, and once its affect wears off the foal will need vaccs. The easiest time to do that is during weaning so doting momma doesn't give everyone a hard time while they are handling the foal.
After the mare dries up there is no need to separate them unless you have a ravager in your herd, in which case both should be separated together. The foal needs to be with its mother for at least 6 months - ideally a year, to give her time to school him. If they are together, he should be gelded NLT 6 months...
Last edited by Faceman; 08-03-2011 at 06:51 PM.