I'm not sure how to do this either. Our daughter's dog had a complete conniption fit as a 4-6 month old puppy getting a rectal temperature taken. The vet's office person told them the same thing, something along the lines of, "Oh, you're going to have to work on this at home or she'll be too hard to deal with when she comes to the vet. She' is trying to bite us." My daughter called me in tears because they had suggested her sweet little puppy was an aggressive monster. We got a lot of good laughs trying to figure out the best way to acclimate a puppy to having her rectal temp taken.
"OK, start practicing with a toothpick, then move up to a matchstick, then try a mechanical pencil, then try a Sharpie..." We got pretty crazy with suggestions, of course, none of which were tried and the pup never had another issue at the vet's office with getting her temperature taken.
For toenail clipping, probably all you can do is repeatedly play with his feet and toes, getting him more accustomed to having them handled. Some dogs still despise getting their nails clipped. I think one of the breeders on here even takes one of her dogs to the vet to get his nails done because he's so difficult to do at home. If a breeder has difficulty, what hope is there for us regular folks?
In my own opinion, short of doing what you're doing, I don't know what else to try and I think the vet's staff should maybe be better trained in making the little beasts comfortable and not saying such idiotic things to the new owners.