First, the little fish right away.
If you hide the sidebar, then show it, you should see the fishy links.
If that's working fine, then you are probably missing the "Startup Actions" tiddler. Copy that over, save your TiddlyWiki, then close it and open it again.
Do take a look at that Startup Actions tiddler. Adjust that tiddler accordingly if you want the sidebar to show on startup.
The fishy links are setup in my TiddlyWiki as links that only appear in "Author Mode", but disappear in "Reader Mode". To keep things simple, hiding the sidebar is "Reader Mode", and showing the sidebar is "Author Mode".
If you want the fishy links to always be visible, then adjust the templates accordingly.
Now, I'm checking out your TiddlyWiki so that I can help you out with #3.