"Override all security" - Must be Forth!

I think java swing is a very good way to handle this. PHP is very powerful and probably could handle everything you need it to do. Fox Toolkit or QT would work well if you don't mind C++. Not sure about licensing issues mixing QT with an open source project, I haven't had need to research that before.

We took measurements of everything and put it in visio to scale. An overhead view and at least a front view of each rack works well. That's for the visual part. For the connections, use a database so it can be easily queried and traced. Full dependency reports may take some SQL wizardry, but can be accomplished if the DB is carefully designed.

I've been using various versions of MySQL for about 7 years now and have had no issues at all. I don't use InnoDB, stored procedures, or subqueries, so I can't speak to those features.
I have used replication, extremely long queries, complex joins and unions, and all other common features with no problem.
I took many precautions like daily backups, log storage, etc. and never needed them except for restoration of lost data due to user error (user sent query that deleted all entries, or updated all entries, etc.)
I have a couple programs I haven't touched in 3 years except for minor cleanup that are still running with no problems.
If you're running into issues with MySQL, you must be using new features or versions that just aren't as rock-solid as core MySQL is.
I must admit that by design my programs don't run into many concurent update collisions and if they did, it would only be a minor annoyance.