Through an experiment, I discovered that I could reference a stylesheet using the <link> with href relative to the location of the .java file. This relates to question No. 1, mentioned in the question, but personally I think that it is too bulky and probably will not use it. He also does not solve problem No. 2 (if anything, this makes it worse).
I am still open to suggestions for the best solutions! I suspect that the full implementation of what I really want to do will require the Eclipse plugin.
[project root] /src/org/foobar/Foo.java:
package org.foobar; public class Foo { }
[root project] /javadoc.css
p.orange { color: orange; }
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