Oh my, it could be SO many things. Is there a lot of corn in his kibble?
Do you put the good smelly powder on your floor? (A BIG cause for this).
Do you have an automatic air freshener being sprayed ANYWHERE near him?
Do you use Fabreeze?
Do you use fabric softener on his blankets?
Ok, you probably see where I'm going with this. What I would do if it were me...
Not get the shots for a while. Bath him and rinse him really REALLY well. IF you have used the powder on the carpet, vac it and shampoo it. Make sure to rinse it several times. IF you have used good smelly stuff on your furniture, shampoo it also. IF there is a lot of corn in his food, do a slow change-over to a better brand (corn makes Yorkies itchy). If licking himself has become a bad habit due to the rash, put an e-collar on him for a while. I'd hold a cool wash cloth on his little "privates" to help ease the irritation.
Please let us know how your little boy does.