Does anyone have seasoned and sound advice on running a civilian security operations command center (Policies & SOP's)?

If you're setting up the security ops center from scratch, you're off to a good start asking for advice, other organization's SOPs, etc. From a process improvement guy's point of view, here some things you should consider:
-Know you customer (possibly the CEO, CFO, CIO, owner, and/or board of directors) and understand their quality requirements
-Map out processes first, then write SOPs including standards. Use the SOPs for training and the standards for evaluation of both the process and the people.
-Exploit automation: within your budget, use as many automation tools as you can to reduce labor and increase accuracy. Anything and any one can be spoofed, but top quality IT tools are probably harder to fool than people.
-Continuously test your processes and revise as needed to ensure quality standards are met
-Humans are the weakest point in your security apparatus. "Human engineering" can be used to breach your security. It's amazing how many secretaries or executives will give up their user ID and password to a well scripted and smooth tonged hacker.
-ID cards and passes will be hacked, counterfeited, and stolen. Have a way to verify IDs that looks for these problems.

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I was a CENTCOM Joint OPS Center XO back in the day (best job I ever had)..... Best advice is don't re-invent the wheel. There are other OP CENTERS. Look at how they are set up, and tailor it to your needs. You can spend a lot of wasted energy building something that might work, instead of massaging something that is already proven to work. Also, and this sucks, but get rid of people quickly that aren't following procedures or do not work well with others. They will cause too much strife in the long run. Move them out of the OPCENTER and into a support role. Lastly, get the battle rhythm right with regards to what watch rotations are, when reports are due, etc.