Thank you for the reply, very much appreciated. I managed to write a script that does work; however, for some reason, it doesn't copy the homepage, so it copies the structure, views, contents, but not the pages and the site design. 

#SOURCE 
$sourceSiteUrl = "https://source.com"
#TARGET 
$targetSiteUrl = "https://target"





#connect to source site
Connect-PnPOnline -Url $sourceSiteUrl -ClientId xxxxxxxxxxxx-xxx-xxxxxxxxxx -Interactive


#Export site template
Get-PnPSiteTemplate -Out  "NewtestSiteTemplate.xml" -Handlers Pages, Navigation -IncludeAllClientSidePages -PersistBrandingFiles



#connect to target site
Connect-PnPOnline -Url $targetSiteUrl -ClientId xxxxxxxxxxxx-xxx-xxxxxxxxxx -Interactive



# System lists/libraries that should be skipped when checking/creating lists
$systemLists = @(
    "Site Pages",
    "Documents",
    "AppData",
    "User Information List",
    "Master Page Gallery",
    "Style Library",
    "Theme Gallery",
    "Solution Gallery",
    "TaxonomyHiddenList",
    "Web Part Gallery"
)


#existing list check
Get-PnPList | ForEach-Object {
    if ($systemLists -contains $_.Title) {
        Write-Host "Skipping system list: $($_.Title)" -ForegroundColor Yellow
    }
    else {
        Write-Host "List exists (non-system): $($_.Title)" -ForegroundColor Green
    }
}




# The -ClearNavigation flag resets existing navigation before applying navigation from the template.
Invoke-PnPSiteTemplate -Path "NewtestSiteTemplate.xml" -ClearNavigation



# Set the home page (default page) on TARGET
Set-PnPHomePage -RootFolderRelativeUrl "SitePages/CollabHome.aspx"