I can't answer a lot of what you ask about accessing the JCR in another webapp... etc - but I can talk about the DataSourcePersistenceManager and setting up a MySQL database backend - since I've spent some time working on getting my build process automated and getting this working reliably.
Is it possible to use a JNDI connction pool without DSPM ? According to the wiki, JNDIPooledDatabasePersistenceManager is more stable than DSPM, so why don't you use JPDPM instead of DSPM ?

Here are some notes I have for you that may or may not be helpful. I'm being brief here, but if you need a better explanation let me know...

You DO create the file in ${CATALINA_HOME}/conf/<hostname>/<webappname>.xml to get the DataSourcePersistenceManager working properly. (I've tried to put a context.xml inside the META-INF/ dir of the war file that had the same contents as what I put in the conf directory, but it didn't work for some reason)
I see, does it work if you add the configuration to the Host Context section in the server.xml ?||

If you are building 3.0.3 (or whatever version) from scratch, you can run "mvn clean install -P webapp" and it will generate an exploded war and the war file in the magnolia directory
I run magnolia with Eclipse / WTP (I have a worflow problems with it : http://www.nabble.com/Workflow-exceptions-after-restarting-Eclipse-tf4341298.html)

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