Yes. Set imageClickMode="OPEN_URL" (in JuiceboxBuilder-Pro's 'Customize -> Main Image' section) and, when a main image is clicked, the corresponding linkURL will be opened in the linkTarget window. (Ordinarily, when setting imageClickMode="OPEN_URL", the corresponding imageURL will be opened but if a linkURL has been assigned to the image, then this will be used instead.)

You can specify a unique linkURL and linkTarget for each image on JuiceboxBuilder-Pro's 'Images' tab.
Just click a thumbnail and the linkURL and linkTarget input boxes will be visible below the thumbnails.
(Otherwise, you can edit your gallery's 'config.xml' file manually in a plain text editor to add your linkURL and linkTarget entries as attributes to the <image> tags.)

A linkURL can be relative (to the web page containing the gallery's embedding code) or absolute (in the form 'http://www.example.com/files/file0001.pdf').

If you want to use imageClickMode="OPEN_URL" (to have the image click open the image itself) but still have a link somewhere to open a custom page, then perhaps the best course of action would be to create unique links in your image captions using HTML formatting as documented in this FAQ.
Image captions can be multi-line (using HTML line breaks <br>) so you could keep your existing captions and add something like the following to the end of them:

<br>Click <a href="/custom_pages/page0001.html" target="_blank">here</a> for more information.

You could then create your custom pages in Showkase (if you like) and hide them from the navigation menu by dragging the pages onto the 'Hidden pages' tree node on the 'Pages' tab.

I hope this helps.