Plugin Recommendation
I’ve had some great experience with the plugin Custom Post Type Permalinks.
Here’s the settings panel that it provides which allows you to define your structure per custom post type.

Adding More Permalink Tags
If you want to further extend the permalink structure tags for your needs you can take a look at the add_rewrite_tag API function.
CTP Tax Archive
The CPT Permalinks plugin won’t take care of your CPT Tax archive, so you need to add the following rewrite rule to your functions.php file:
add_rewrite_rule('^(your-cpt)/(taxonomy_1|taxonomy_1|taxonomy_3)/?','index.php?post_type=$matches[1]&taxonomy=$matches[2]','top');
You will obviously need to replace your-cpt and the taxonomy names in the regex.
Testing
I highly recommend you to use the Monkeyman Rewrite Analyzer to help understand what rewrites are registered and how they match your URLs.
Hope this helps you out.
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