Normally there is a fixed setup charge (say 15 min), to get the plate on the machine and to program the toolpath. Then there is the cost of the material. Customer pays the fraction of the price that the whole plate was purchased for, based on the area he uses.
The cost of the job is the running time of the program (total perimeter cut/feedrate).
Then there is the cost of the consumeables (you'll know after a while how many inches you can cut). Then theres heat, rent, electricity, and last of all your profit.
I'd start by billing out the machine at $75/hr, and see where that leads with your example....
regards
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Can't Fix Stupid