Rebel was neutered at 5 mos and had the same problem. Neither of his testicles had descended. The vet actually found one in the crease where the thigh starts
The hardest part with him was trying to keep him from being too active when I brought him home. He was back to normal basically the next day. (He also had 3 baby teeth removed at the same time)
I'm sure he'll be fine and it sounds like you've got a very good handle on the other issues.
Your baby is going to be a great addition to your family. Welcome!