Probably the easiest way to make the transition is to first be sure you have his indoor cage and area chosen and prepared. Whatever area you plan to house him should be the same place where he will eventually be allowed to roam. The idea will be that eventually you'll be able to just open the cage door to allow him out for exercise. Of course this also means bunny-proofing that area.
Once everything is prepared, it would be best to just bring him indoors. Don't try to "transition" him by bringing him indoors and then back out over a period of time. That would be more stressful and also harder on his system since it is difficult for bunnies to maintain their body temperature. Switching back and forth between temperatures (outside/inside) would be stressful.
Once he's inside, just leave him alone for a couple days. Don't try to pet him or reach into his cage (except to refill hay,water, etc). Don't change his litter box either. Just leave him be for at least two days. This is the time he will start to acclimate to his new home. He will be in his new cage becoming familiar with the new sights, sounds and smells of indoor living. Go about your usual routine around his cage. This way he gets used to the 'new' normal.
I have a section on my website that details more about bonding with your bunny. That will save me from typing more here. It explains how to let bunny set his own pace for getting to bond with you. It's here
You already know that you'll need to go slowly, so it sounds like you'll be well on your way to life with an indoor bunny. It is so much more enjoyable (imo) to have bunny indoors with the family. My bunny, Mocha, just hopped on the couch by me a few minutes ago to 'ask' for his nighttime treats. Now he's sitting on the floor a few feet from me and watching me type.