I totally relate to your problems since they are all exactly the same ones I have encountered and continue to encounter. Installation was much more challenging than it need to be and after I was done I was left thinking, "How do I use this?"
Your assessment of the user's guide is kind. I find it badly organized and outright misleading. The specific references to deliverables (the conf files and the uploader jar) which are absolutely NOT delivered in the current bundle are an outrageous time-waster. Why not just take two seconds and bundle them into the distributed zip?
Key parts of the installation are broken up into distant sections of the guide, like the license info that needs to be included in the conf files, which are "covered" much earlier in the document. The status checks will absolutely fail if you only follow instructions up to the point they tell you to run them.
You couldn't log into the admin console? No surprise. That's because the default password, park345, is not supplied in the user manual or anywhere else. I had to ask. That was another lost 24 hours. Frankly it doesn't matter, though, because there will be nothing in the admin console until you manage to get some books in there. You thought maybe you could add PDFs that way? Me too. It would make sense wouldn't it? Sorry, but no.
The jar file that Adobe refers to, but does not supply, supposedly allows you to do that, though I have not gotten it to work.
The syntax for it, since Adobe does not bother to provide any full, real world examples, is:
java -jar UploadTest-1_1.jar http://yourdomain/packaging/Package /localpath/your.pdf.
You can pass flags to indicate the presence of things like an XML file that controls the permissions or a thumbnail, e.g.
java -jar UploadTest-1_1.jar http://yourdomain/packaging/Package /localpath/raw.pdf -xml -jpg
You don't tell it the name of the XML or jpg. You are supposed to use identical filenames and locations as the PDF or Epub.
Even though I figured all that out I still get an error when I run the thing:
There was an error with the Package Request
It means nothing to me and the logs don't help. Maybe someone reading this can kindly tell me what to do since the manual leaves me nowhere and I am still waiting for email support on this issue.