Dear E.,
I went through this same thing with my parents when my son was about that age. My mom and step dad had been married for 15 years. He was the only "Grandpa" my kids really knew as my father, "Pappaw", was on the East coast.
My daughter is 10 years older, so she understood. Even still, we didn't get into the logistics of everything with her.
We didn't really say much to my son about it. My step dad stayed in their home as it was his before they married, and my mom moved in with my sister and her family for a time. We live an hour away from where my mom lived, so my son was just happy to see her more often. He didn't really ask too many questions. On holidays, the kids and I often stay at my sister's and I remember my son being so excited when he said, "Nanny, I wish you could spend the night too," and she said, "Honey, Nanny IS going to spend the night and we're going to have some fun!"
He never thought a thing of it. He did say one time that he wanted to go to her house and I said that she didn't live at that house anymore. She had a new house now. So, I took him to her new house. She had just got settled in, but her familiar things were there and he thought it was a good new house. Grandpa did call us from time to time and we saw him on occasion. But I guess as long as my son knew that Nanny was okay, he didn't worry too much about it.
The main thing with little kids is that you don't want to give them too much adult information. You know, TMI....Too Much Information.
You don't mention how close the relationship between your son and your step father is. That, I'm sure, might make a difference. I mean, if they were pretty close buddies, hopefully your mom won't mind if Grandpa stays in touch once in a while. I know that my mom had no problem with that.
Either way, I think the main thing is not to make too much fanfare about it. Little kids just want to know that people in their world are okay. And in your case, Grandpa is fine...he got to go on an airplane (or whatever) and go travelling around a bit. If your son asks why Grandma didn't go with him, you can tell the truth and say that she didn't want to go, and it's okay, because she wanted to stay and they are both happy that way.
This age is way too young to explain divorce or why sometimes people don't stay married or all of that. It just confuses children. Hopefully there won't be a "new" Grandpa to explain in the near future. LOL.
Like I said, bottom line is that little kids just want to know everyone is okay and their world is safe and nothing really has to change as far as it concerns who loves them and takes care of them.
For your "emotionally intense" son, the less you say is probably for the best.
Best of wishes and good luck to your Mom. My mom is doing great on her own and so proud of herself.