Can you get another copy of your rabies certificate with the microchip number on it? All of the PETS stuff needs the microchip on it, basically, so that it's really obvious what happened to what animal (and everything can be cross-checked against the actual chip in the animal).
I don't know if it will be a problem, because my vet put the chip #s on the certificates, but I do know that my vet here in London said that if they weren't on the certificate, she wouldn't have been able to issue a pet passport (EU) for my pets without re-doing everything (including the bloodwork/6 month wait, I think).
If you have documentation from your vet clearly stating the date the microchipping was done for your kitties, and that date is before the date on the rabies vaccine, you should be fine. Otherwise, I would go ahead and get the letter from your vet, just to be on the safe side.