This is generally what I do. I'm also no stranger to writing sections with [WORDS] or [DIALOGUE] as placeholders in between so I can get what I am able to write done first.
But it's a familiar process, knowing what you want to do and then it doesn't quite come together for a while. But also the sense that it will. I was having a discussion with a visual artist friend over on Facebook a short time ago about that nagging feeling where you can see the seams even when others enjoy your work but believing in your ability even with that nagging voice is really the key. And it is.
Sometimes I'm in love with my paragraphs and sometimes I have a bunch of unrefined scraps. 
I do the same thing.
And I'm terrible at naming things, so currently my notes read something like
ME: "The political plot here involves 'Poland' trying to secure an alliance with 'Hungary', to fend off the advances of the 'Byzantines'."
ALPHA READER: "But...but those countries are nothing like-"
ME: "Fake Poland's flag has red on it too."
ALPHA READER: ...All right. And the other countries?"
ME: "Er...Both Hungaries are to the north. And maybe they're sick of puns about their countries' names?
"
ALPHA READER: "Riiiiight."
But usually if I hash out the scenes that interest me, I get a feel for the flow of a chapter and can come up with interesting scenes between the stand-out ones. It just looks real messy for awhile.
I do it this way too! I usually work on 3-4 chapters at the same time, because I come up with several pieces of the story with huge gaps in between, and write down the pieces I am certain about at soon as I think of them. Then I slowly fill in the gaps. I think it makes sense as a creative process, because it adds unity to the entire work. Didn't the visual artists say something similar earlier, that you're supposed to work on the painting/drawing as a whole and not spend all your time on individual parts?
Also, to me the story always emerges as a dialogue first. I have a thing for dialogue, it takes up most of my writing, and it somehow takes me less editing to end up with something I'm content with. So lately I've just been writing the "skeleton" of a chapter as if it is a play, with everyone's lines. Then I fill in all the "he said", "she laughed", "everything exploded", etc.
Now, one downside of this is that if I get stuck on one little piece of the puzzle, I won't consider the entire chunk of 3 chapters completed, so it's really hard for me to actually finish anything. I have a Google Drive fodler called "Loose fanfiction bits", which is filled with chapters that I worked on and eventually paused. Some of them are trash but for some I'm just missing a few things that I can't figure out how to write.
Right now I think I almost have down the first 3 chapters of my fic, but I can't be truly done, because I'm stuck on... the description of a room. Seriously, at some point I need to describe Lavellan's quarters at the Temple of Mythal and I can't come up with anything. (She even mentions at one point that she hardly spends any time there, so I guess she truly doesn't care, lol.) It's very frustrating, and I've been struggling with it for several days. If anyone has any advice on how to generate passable room descriptions, I'd be so thankful! Stupid Temple of Mythal bedroom is stupid. 