Hi Aram. Sorry for the delay in getting back.
So you are getting an issue with mysql connection failure?
One thing you could try is setting the query mode to xmlpipes. When you do this, the search daemon doesn't attempt the connection itself, so you eliminate that. Instead, it calls a sapphire controller to get an XML structure that it indexes instead. An advantage of this is that you can run that controller yourself, and see what data is being fed through. To see the command to issue, switch to xmlpipes mode (just set the $sphinx static, setting "mode" to "xmlpipe") and dev/build. If you look in sphinx.conf, it will have different source sections, which contain a command line that sphinx will execute to get the xml. You can run this command yourself. This can help to identify if the right data is being indexed, or if its an indexer configuration problem.
I've used sphinx on a few sites now. The external environment is the fiddly part, getting permissions and paths right. I tend towards using xmlpipes by default, and add in the messagequeue module so offload delta reindexing from the user request.