Hijacking my thread back. To answer all the questions in one go:

From Chad Nelson:
> What version of WP are you currently on?

Embarrassed, but you just have to do a view source of the Journal to learn
the dirty truth: WordPress 3.0.4

As you can see from the wiki, upgrading is something we want to do:

  http://wiki.code4lib.org/index.php/Code4Lib_Journal_Tech_Wishlist

> Is the source of the plugin available anywhere?

Version 1.4.3 is the most current version I found. There's an older version
on a Google Code repo, so don't use that.

  http://wordpress.org/extend/plugins/issue-manager/

From Jason Stirnaman:
> It might be worth considering the Annotum theme for Wordpress, meant to
do just that.
> http://wordpress.org/extend/themes/annotum-base

Peter Murray suggested Annotum to me last week, but we'd very likely have
to change our workflow to use it and work would have to be done to merge
our template with Annotum's.  I'm not against either, but inertia sets in.

Peter also mentioned SemiotiX New Series, which I have yet to suss out

  http://ideophone.org/semiotix-wordpress-e-journal/

From Shaun Ellis (echoed by Katherine Lynch):
> Tom, can you post the plugin to Code4Lib's github so we can have a crack
at it

I can't, since I do not have a login to that Github account (I didn't even
know about it until last week). I'm not sure what the feeling of the
current Code4Lib owner(s) is regarding this, but if you can push content to
that account, please feel free to start a new plugin repo there.

I've had offers of help from Mark Pernotto and Katherine Lynch, for which I
am thankful. We'll have to figure out how to go forward with this. First
though, Mark and Katherine, can you confirm that you will help? We can
probably do the rest of this off the public channel.

And to anyone else who feels like it: please take a look at the code in the
WordPress Codex and see if anything jumps out at you. All and all, it
seemed to me to conform to the WP documentation I've read, but obviously
something has changed in the codex that I'm missing. Mark suggested that
the way WP handles jQuery & ajax requests might be part of it, and I think
he's on to something. However, there also seems to be a problem with the
way the cat_ID (category ID) search is being executed to build the list of
articles in the target issue. Maybe it is tied to the how the
jquery-ui-sortable-1.5.2.js module is working, but maybe not.

Thanks for the positive response,
Tom