It's not at all odd that Mr. Snake might have a poor first shed, a lot of them do until they adjust to better husbandry and you will likely be tweaking that here and there as you learn what works best for him. There's a great sticky here about how to help if he has a poor shed.

Probing or popping by your herp vet won't be at all traumatic. It's over very quickly and really the snake doesn't fuss much about it. They wiggle a bit but that's more I think from just being restrained (all pets do that at the vet in my experience, snake or not).