Slightly off-topic, but with a similar end-purpose: I've been thinking that I'd like to add new PoIs on the Kelestia pdf map (which I have), mut is this even possible? Maybe with a new layer: user-defined PoIs. This way I could mark what I own (eg. Chendy), or other places what I've defined in a campaign, or that I have maps for and have read the articles (for fanon), so I know when players are near/at a mapped area. If that can be done (I've yet to try editing pdfs, was going to have a look for my character sheet project), a Harn-only version of this project isn't that useful for me. A seamless Venarive- or Lythia-wide (or even Kethira-) map would still of course be wonderful, so keep at it
At least in Adobe Acrobat Pro 9 you can add comments on top of the map. You can move them, change the color, opacity, symbol and add text to hideable text box. You can't, however, change the size of the symbol, which is a drag. Another possibility is to add text labels. You can defin where the arrow points, but the text is visible at all times. I didn't play with those much, but at least in theory it is possible.
Didn't find a quick way to introduce a layer (you can import a file as layer, but that's probably not handy), but I guess (didn't check) you can hide/unhide the comments from the menu.