I think you're doing some re-work around the standalone distribution and the JIRA home directory anyway, but I thought I'd raise this anyhow:
If you download standalone, and startup go into the bin directory and run startup.sh, JIRA will create a jira_home directory inside the bin directory (containing all the plugins framework stuff) as well as one on the top directory. It doesn't seem to read the directory in the bin directory however, which causes some ClassNotFoundExceptions.

At the moment you have to start JIRA standalone by calling ./bin/startup.sh from the top directory. You can't cd bin ; ./startup.sh.