welcome to YT. I see that you said he could have the rabies shot in 3 weeks, which will make him 12 weeks old then...I really still think that is too early. most are around 16 weeks. I would call and get a 2nd opinion from another vet in the area! Let me mention...I have always heard that the dosage of the rabies shot is the same for a 3 lb yorkie baby as it is for a 60 lb dane puppy...so to me, the longer you can wait to get it, the better. it just seems like a lot to give a pup.
good luck

can't wait to see pics of your baby and watch him grow