this system has 2 cabinets... one has the processor... they both have AC/DC switches
1 - does it matter which sequence to turn them off and on?
2 - I rebooted both and the phones are working great, BUT now there's a clicking that I think is coming from the primary power supply... what do you think?

You only need to turn off the main cabinet which is the left cabinet. The clicking noise is probably the message waiting indicator an analog port. If you have an RSTU, BSTU, BSLU card then that's probably where the clicking noise is from. It's not uncommon for the feature to be accidentally set. If you know what port it is set on, you can go off hook and dial #409 to clear it.