pipes are problematic separators ... compared to something like bullet points

Fair enough. This will require modifying CSS in a static file, so will take some time.

When the line breaks are removed the menu wraps smoothly

Done. Feedback requested. :-)

Turning off text-decoration (underline) on links ...

I don't know about that. We need to make accessibility a priority. I would want any change to ameliorate it, or at least not pejorate it. :-D

integrate the monkquip with the blue page header

Maybe.

Need Help?? One question mark

It's been that way since the beginning, and I think falls into the category of "fun, quirky stuff that makes PerlMonks distinctive".

Thank you for your suggestions!