Hi George,
I would have thought this functionality is limited to HTML/JS.
If you want to include custom php, you will need to delve slightly deeper into moodle code.
This article/book/ we goes over the process of creating a super simple plugin. I recommend following this through to 'Line 11: Starting output' at least, here he mentions the process of loading and outputting blocks (which are plugins in moodle too).
I am no developer, but since this was unanswered I thought I would have a crack (I found this link very useful not too long ago). I dont know what you mean by CMS.. I would have thought you could have all your 'issues' within a single block and therefore bundle all your code within a plugin (checks for issues, displays those relevant or nothing at all).
If you want to organise blocks in a CMS, this would be a much bigger undertaking. I think (plz correct me if im wrong) you would have to fiddle with the code responsible for rendering blocks.