The solution for the two stylesheet problems is to make one small change each to the build.xml file and the docs.properties file.
Adding the following line at the end of docs.properties gets rid of the absolute path:
This results in the following output:
<link href="commonltr.css" type="text/css" rel="stylesheet" />
And fixing the following target in build.xml includes the stylesheet in the output directory for each document:
<!-- build to temp directory, then move the files over to the correct -->
<!-- directory name, prepending the Apache License as we go. -->
<replaceregex pattern="Web Sample" replace="$
Changing the includes line to the following causes the stylesheet to be copied to the temp directory and therefore to the final output directory:
Including the stylesheet improves the formatting of the HTML pages: It inserts vertical spaces above notes and the topic links at the ends of topics. It puts the terms in definition lists, as well as the introductory words in notes ("Note" or "Important", for example) in bold. It also reduces the size of topic heads and slightly increases the size of sub-heads.