Dear Benny,
I have been out of town for a few days and just saw your posts. Sorry I wasn't here when you were making the marmalade to offer suggestions or clarify the recipe. Sounds like you got it to work just fine anyway.
So glad it turned out well with your creative adjustments. That is the type of thing I would do also. I don't know about vanilla in orange marmalade, but I put it in my peach preserves, and can't imagine now not having it with it. I might take one serving and add a tiny drop, say dip a teaspoon in vanilla and then stir the marmalade and give it a try. Doing it that way, you won't be wasting precious marmalade if you don't like it.
When the recipe was talking about the seeds and scraps, I assumed it meant the ends you cut off of the oranges. I would not process seeds regardless of what the recipe said, unless it was a pomegranite where you can actually eat the seeds. I think this processing was just to increase the liquid for the mixture then it is strained.
The whole slices that were boiled, are removed from the liquid, and the pulp removed and the rinds returned. I like the pulp in my marmalade, and would probably process it and return it for a thicker marmalade. That is what I have done in my regular marmalade. Since the white inner peel has pectin, I think that is the reason they have you boil it and then remove it for this recipe. It allows you the benefit of the pectin without the fruit pulp so it will thicken. I also don't think I would be using the cold water rinse on the peels to remove the pulp if I want to remove the pulp. Seems that would remove some flavor also. I would probably just let it be messy and use some rubber gloves.
This is my thought on it anyway.
Eat a slice of toast thick with marmalade for me.
Jean
PS now you have me in the mood for marmalade, I may have to make some type just to satisfy the craving.