What a weekend, after killing off the setup I had working really well and trying out some other options. I came to the conclusion very quickly that the setup I had was the best one.
Our HP Microserver N40L with Ubuntu 12.04.x and LXC (Linux Containers) worked best for us. We have our mdadm based software raid, and have Linux containers do other services as needed.
So I am in the process of reinstalling everything back as it was, I am very glad I made good notes for most things including LXC.
If anyone want’s more explicit details, let me know in the comments and I can post further follow ups with more details on what we do and how we are doing it.