Others will arrive I think. Because I can't absorb this yet, I'll just show my 'inspiration photos' cause seems you're in process. ;)

In other words, wondering if there's a way to prevent moving glass around.

What is plan for the small nook with window?

I’m closing the two little windows up for cabinets. The two little windows I
The family room are closing up too.

The nook will just be wall all the way down.

This is hard to follow. Need an existing floor plan and the suggested.

It’s basically a clean slate. Everything will come out.

Big changes -- what will nook's purpose be I can't tell what [after you 'wall it up' I guess]...

You have 2 high windows already there -- must be a way for your slider, and keep the 2?

Brainstorming that you have a a cool look of continuous glass [above uppers], like here?

Modern Micro Residence · More Info

This is like your idea-- an option for continuous glass, sleek look? where slider will be, and with new lowers next to it?

LaCantina Doors · More Info

Idea for stools right outside the new lower cabinets -- and a small regular door next to it, like here. If you serve alot from kitchen to patio, could be good to look into.

Midcentury Riviera · More Info

My Houzz: Full-Tilt Reinvention for a 1950s Ranch · More Info

It's a bit confusing and the pictures don't really tell us much. Could you please do the following:

(1) Draw up a fully-measured layout of the Kitchen space. Include the widths of each wall/window/door/doorway and the distances between each wall/window/door/doorway. Include trim, if any, in the window & door/doorway measurements.

Use your existing windows, doors/doorways and indicate which ones you think you'll be closing up and where you're thinking of putting in new ones. See the end of this post for an example of what we've been asking for.

(2) A sketch of the entire floor with all rooms labeled. While it doesn't have to be to scale, it should at least be an accurate depiction of how all the rooms relate to each other. Not only will this allow us to see how the Kitchen relates to the rest of the home and see how traffic flows in, around, and through the Kitchen, but it will also help us see some of the issues you're concerned about and offer suggestions for dealing with them (e.g., sight lines and transitions)

Taken from:

FAQ: How Do I Ask For Layout Help & What Information Should I Include?

• https://www.houzz.com/discussions/5500789/faq-how-do-i-ask-for-layout-help-what-information-should-i-include

You can draw it by hand also.

A measured drawing will give us a better idea of the three spaces. Label the items that will be changed or removed.
I, personally, like my kitchen to be visually separate from the dining room because I can be a messy cook using a number of pots and pans, and my guests don’t need to see that. I have always had a separate, dedicated “formal dining room”. The family dining space can be a separate breakfast room or a real table and chairs in the family room. I don’t like bar stools in the kitchen.

I have no idea what you are planning from these pictures . Post a detailed floor plan to scale