I couldn't really find a way to contact you directly or submit a bug fix, so I guess this will have to do. I have fixes for three issues that I have come across.
I have an updated .htaccess file that fixes an issue inherent in WordPress that causes url's to Nested Networks' Sub-Sites to break. WordPress' mod-rewrite directives were not setup to handle anything past 1 level of nesting.
There is also a function to fix an issue within the Networks plugin that causes some of the path information within WordPress to get corrupted when adding Sub-Sites to a Nested Network (like in the example above). This has to do with the $base variable I was talking about in the meeting.
The final fix is in the networks-admin.php file at line 438, which fixes an issue where a link was hard-coded as http and was causing redirects back to the base https domain.
Email me at [ redacted, support is via the forums and not email ] for the code. : D