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I'm making the switch from SharePoint classic to modern sites.

When using classic I had created our own custom "theme". I would go into SharePoint Designer 2013 and upload our HTML file which would create a MASTER file. I would then set that to default and upload all our assets + CSS files to the site and just like that our own custom theme.

Now looking at modern site, I see that I can upload my own theme via powershell, but that theme looks like it's more of branding. Changing colors and whatnot. What I'm trying to do is change the structure of the site as well. How the header is being displayed, body, content. Can someone point me to the correct documentation to get this done? Here is what I've been reading so far:

https://docs.microsoft.com/en-us/sharepoint/dev/solution-guidance/modern-experience-customizations-customize-sites

https://sharepointmaven.com/how-to-configure-and-apply-a-custom-theme-in-sharepoint-online/

https://support.microsoft.com/en-us/office/page-templates-in-sharepoint-faa92408-0c84-4e3d-8460-3c28065e7873

UPDATE: Looking through some tutorials I found this link here: https://developer.microsoft.com/en-us/fluentui#/styles/themegenerator?fabricVer=5

However, this too looks like it's only for colors/branding and now changing site layout/structure.

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As Hugo Bernier says:

If you need to customize the look and feel of modern pages, you can use custom tenant branding, custom site designs, and modern site themes without incurring the wrath of the SharePoint gods.

If you want to go even further, you can use SharePoint Framework Extensions and page placeholders to customize well-known areas of modern pages. Right now, those well-known locations are limited to the top and bottom of the page, but I suspect that in a few weeks, we’ll find out that there are more placeholder locations coming.

SPFx extensions are only limited to only two placeholders: header and footer:

enter image description here Credits to Chris O'Brian, "Use an SPFx Application Customizer to add JavaScript (e.g. header) to every page in a site".
Links

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As Denis Molodtsov said, you could use SharePoint Framework to custom modern sites.

For your requirements, I would suggest you use the SPFx Applications Customiser CSS Injection and create your custom css/js file to change site layout/structure.

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