When you say "the main display on the server doesn't show the :8080", I'm guessing you mean this:

If so, then FWIW, the program that displays that is called "Confconsole". All the info it shows there (other than the IP addresses) is static and can be adjusted by editing the text file found at /etc/confconsole/services.txt.

It will likely be obvious what needs doing when you open it, but you'll just need to add the port suffix on the end of the 2 lines you wish to change. I.e. change the top 2 lines from this:

Web:        http://$ipaddr
            https://$ipaddr

To this:

Web:        http://$ipaddr:8080
            https://$ipaddr:8080

To edit, it's probably easiest to log in via SSH and do that at the commandline. TurnKey has vim-tiny (you can install vim "proper" via apt if you're a vim user) and nano pre-installed. People unaccustomed to vim may find nano a more intuitive option. Alternatively GUI lovers may prefer Webmin (it has a text editor).

Re your second request/question; I'm almost certain that is because those URLs are generated on the fly (by php snippets on the index page) and it's not expecting there to be explicit port numbers included (so is generating invalid links; or possibly no links at all).

Depending on how you have it set up and how it's accessible, then the quickest/easiest way may be to just hard code those URLs. Although that may be a bit tricky if your server isn't using a static IP and/or a specific domain.

The other option is to edit/extend the existing PHP snippets so that they return something useful in the creation of the links. TBH, I'm not exactly sure how that would go OTTOMH (I'm a PHP novice and would need to do some research and testing before I could offer any suggestions). I suspect that if you have a bit of a google and a bit of trial and error and you could work it out.

The default index file can be found at /var/www/index.php and just in case you mess something up and need to back track, the default contents of the file can be seen here.

Also please note that because of PHP caching, you may need to restart Apache (or temporarily disable PHP caching) for changes to be applied immediately.