Thanks for the additional information.
We are unable to run plugins like WP Headers and Footers. It's a security risk to allow arbitrary PHP or JS code to be run on Commons sites.
It's no problem to install Inspiro Lite. Generally, new theme requests are processed and released on the second and fourth Tuesday of every month. As a courtesy, I've released this one immediately and activated on the test site.
Looking over your custom scripts, it looks like they fall into several categories:
1. There's a bit of JavaScript that adds aria-label attributes to nav items.
2. There's a bunch of custom CSS.
3. There's some JavaScript that seems to initialize an external accessibility-scanning service.
4. There's a PHP filter callback that was pasted here incorrectly.
These can be handled in various ways on the Commons.
Regarding 1: I wonder whether this is actually necessary. You're just adding the aria-label text 'Custom Label', which is not actually helpful to screen readers. I think that whoever built the site was probably testing an approach, but ultimately abandoned it. I think it can be safely ignored here.
Regarding 2: I've pasted it into Dashboard > Appearance > Customize > Additional CSS. I should note that much of this CSS will need to be manually updated for the Commons. First, many of the images are referenced by paths that specifically mention the old URL. The files will need to be re-uploaded to the new site (if they haven't been already as part of the import process) and then the references in the CSS will need to be changed. Second, many of the page-specific styles use the 'page-id-xxx' class, where 'xxx' is the unique ID of the page. When you import items into a WordPress installation, the post IDs change. So these styles won't be correctly targeted anymore. There's a few dozen of these, and they'll need to be manually swapped out.
Regarding 3: I'm not totally sure what this was intended to do. If you need accessibility scanning, you could consider a client-side tool like WAVE https://wave.webaim.org/ or Lighthouse https://developer.chrome.com/docs/lighthouse/accessibility/.
Regarding 4: This was clearly an error and can be safely ignored.
I recommend that the user take a bit of time to see how easily the site can be configured to match the old one. Take a look especially at https://testenglish2.commons.gc.cuny.edu/wp-admin/themes.php?page=inspiro and the corresponding page on the old site. This page contains the theme-specific options that I mentioned in my last message. Unfortunately, it looks like Inspiro's options don't come over cleanly as part of a WP export, and I don't see a tool in the theme to export+import.
If it proves impossible to do the necessary configuration after an hour or two of work, we can explore other options.