I've found out answers to my questions - in the end I called the Animal Reception Centre, and only wish I had done so weeks ago instead of emailing with different pet transport companies.
ARC says the Annex II form gets prepared by the local vet & signed by the USDA vet, then closer to the flight date, local vet completes the tapeworm portion. USDA vet does not have to sign off on the tapeworm portion. ARC person verified this with someone else just to be sure.
Rabies vaccine doesn't need to be administered within a certain number of months of flying - as long as all boosters have been given on time, with no lapses, it's good to go.
I believe each airline has different rules regarding how animals can be presented to them for transport. I've decided to fly my dog on BA, and accdg to BA, will be allowed to hand over my dog & his paperwork directly to the BA cargo person. They'll weigh him/his crate and check over his paperwork, and give me a final price based on the total weight. At check-in, they collect all fees (airline ticket, taxes, customs clearance). My dog is apx 16lb and they estimated the fee to be about $1300.
ARC said to fax them all the paperwork once completed for review & they'll let me know before flying if any corrections need to be made.
BA works with JCS Cargo; they are a customs clearance agent & will handle getting my dog cleared through customs. BA doesn't allow the public to do this themselves.
Once the dog is cleared through customs, BA's animal transport person will take my dog to the ARC, where he'll be checked over, watered, fed, etc and released to me upon final review of his paperwork.
You are *not required* to use a pet relocation company unless you feel you need professional help in getting the microchipping/rabies/paperwork requirements handled on your own. Of all the ones I emailed for info, the agent from Petrelocation.com was by far the most helpful. These companies specialize in complicated moves or those where the animal can't be moved at the same time as its family. If you do need help, I'd highly recommend Petrelocation.com (specifically Matt), but it is a completely optional service, and absolutely not required by the ARC.
Hope this helps!