Every 5.5 hours I want port 5 to turn on/off. The power only needs to be cut off for a couple seconds and then turn back on.

Try this:

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ReefAngel.Relay.Set(Port5,now()%19800==0);


1) So does Port 5 need to be listed as an "ALWAYS ON" port?

2) Do I paste the code in the custom code area?


Currently I have Port 5 set as an "ALWAYS ON" port and pasted the code in the custom code section. And now for some reason the default of Port 5 is to be OFF? So I have to mask it to turn it on. I figured that I'm doing something wrong.

You can remove the always on code if you want to. Leaving it won't do anything either... So your choice.
I misread your question. I thought you wanted the opposite
Try this then:

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ReefAngel.Relay.Set(Port5,now()%19800!=0);