$600 sounds awfully high...assuming I'd had my dog microchipped as well as my cat, my vet bill from last week would have been ~$180 instead of $135 (includes chip, vaccine, vet visit fee for both pets). I'm anticipating $150 to send to KS, but will know for sure on Friday when I go in, so I will update then (I might get off cheaper if the vet's willing to spend the 30 seconds signing the form "for free" and just charge me for blood draw/shipping, not a vet visit fee as well). Unless your vet is willing to throw in the final visit to do tick/tapeworm stuff 48hrs before you fly AND your vet's normal visit fee is above $20, I'd shop around.
Also, I always go to a low-cost mobile vet for routine stuff, and they do microchipping (they did both the dog and cat years ago, but the cat's chip disappeared since then). You might want to google mobile/low cost vets in your area...mine technically focuses on spay/neuter, but will do a complete wellness exam including annual shots, physical, and rabies (1 or 3yr) for $35 per pet. They charge $15 per pet to microchip. So, in theory, if they would agree to follow the procedure re: chip first then vaccine, you could get both pets chipped and vaccinated for ~$100 total. I doubt they'd be able to do the KS blood work/shipping, but it'd be worth asking. Even if that's $150-200 for your cats at your normal vet, that's still $250-300 total for the whole thing, not $600. I find the mobile vet to be more convenient than my regular vet, as well...I drop my pets off at 8am, and they hang out there until 4:30 (or later, depending on how many patients they have that day) when I pick them up...for me, at least, that fits much better into my work day than taking a 1 1/2 hour chunk somewhere to go to the vet and be there for the full visit. (The only trick here would be that you wouldn't be able to ensure that the vet did the microchip before the vaccine, but I'd bring that up before making the appointment, anyway, to make sure they are OK with being anal about stuff like that.)
I haven't looked into the USDA fees yet, so can't speak to that. However, you'd want to NOT do it now, as the form (EC 998) is only good for travel within 4 months. So if you did it now, you'd just have to redo it again in 4 months when you're 2 months away from the quarantine ending and being allowed to travel.
So yeah, that's my very long-winded $0.02.