I think you're doing great with the carrier. Feeding him in it is a great idea. I would gradually work up to him being comfortable with that, then, when he's eating his last bite or two, close the door, leave it for a few seconds, then open it. Act like it's no big deal.
On the fan...unfortunately we can't take those down and put them into storage. My Mom brought home a cat that obviously had never seen one. She'd walk into the room, glance up, and freeze because that big giant bug-looking thing was staring at her. Then she'd run out of the room. It didn't matter if the blades were moving or not. It just took time for her to be brave enough to go in the room, all on her terms, and realize it wasn't going to bother her.
He's still occasionally side-eyeing the fan but hes doing well otherwise.
He's had his treats in thr carrier again and ive been practising picking him up and putting him in it. I just set him inside and then walk away. A very neutral experience.
Magnus of course is loving the new carrier. He explores it daily. Ghost is also happy to eat inside it though he will be in the smaller carrier for transport.
On Saturday, we plan to get up at 7 and close thr basement. We will have a normal morning with them. Then, about 5 minutes before our ride arrives, we will put Cal into his carrier first and then Ghost and then Magnus. I do want their harnesses on as well which might make it harder but i want them clipped in.