I found I could use a workaround for my character encoding problem. Maybe someone is interested. So see below. If you want to copy & paste from the PDFs using Preview.app or Skim.app you can't use calibre to generated the PDF.

I don't grasp all the technicalities but, in few words, the problem has to do with the encoding: calibre produce PDF with text with encoding 'Identity-H', while Preview.app and Skim.app need 'Ansi' encoding. Then you can: 1) Convert with calibre to HTMLZ. 2) Replace the.htmlz extension of the file with.zip 3) Unzip the file 4) Create the PDF with Adobe Acrobat Pro using 'Create from webpage' (I tried also Word and LibreOffice, problem here they don't keep the internal links). So close, but this is a dealbreaker. A PDF that isn't searchable in MacOS Preview and lacks the ability to copy content is useless to me. Then a lot of PDFs produced by a lot of apps will also be problems. MacOS's Preview supports only a modest subset of PDF attributes and functionality.

It is particularly limited in its font support. IMHO, Preview is too poor a viewer to use it for PDF on a regular basis. The only time I view a PDF in Preview is to see if clients using a Mac with only Preview as their viewer will have difficulty.

When I view a PDF for myself on a Mac I use a good viewer, usually Adobe Reader. Todd's fix worked for me.

Notice that it does increase file size fairly considerably, and requires that you use an embedded font during the Calibre conversion process that Preview can use. I don't have a list of compatible fonts, but Georgia does work for me. If anyone finds a list of compatible fonts let everyone know. There is probably a way to write an Apple Script to automatically replace the Calibre outputted file with a Preview searchable one.

But I might have to leave that to someone else for now. I'll try it with Automator later, but that's about the limit of my ability. Is there a way for Calibre to automatically accomplish this without going through the external process with Preview? I know I'd appreciate it. Okay, figured it out.

Adobe For Mac Free

If you run a Quartz Filter on the PDF after a compatible font is embedded during the Calibre conversion process it will make the content of the PDFs searchable and copyable. I made an Automator script that takes any files and adds an image filter to them that is ostensibly set to reduce the size of images, but I just set it to 'uncompressed' so that there is no impact that I can discern on the images. You can process a ton of files quickly this way.

As for eschwartz’s comment, this isn't just for Preview. This also makes PDFs searchable on my iPad using PDF Expert, in Papers 3 on Mac and iPad, and entirely indexable by the above applications as well as Alfred and Spotlight. For my purposes being able to call up all documents with specific keywords or names through a central interface is absurdly useful, and not possible if I don’t make it compatible with Preview and other applications like it which don’t have the full capabilities of some readers. Not to mention making it compatible with the broadest range of possible applications, not just the newest, leaves options open for other ways of using the file that I might not have thought of yet.

It also has no negative impact on how I use the files, so I see only positives and no downsides for my personal use.