Hi,

> Has anyone setup two instances of MySQL on the same server? One running 
> just a client's DBs? Any advice would be helpful.

That is not answering your question directly, but MySQL works finr
over an SSH tunnel.

You'd have your users connect/authenticate with SSH first to establish
the tunnel, then they'd use the tunnel to forward the NySQl
connection. 

Best regards,

Olivier
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