Don't know if this will help because I run Ox/Fuel & mostly cut 3/8" through 1 1/2" steel plate.
I calculate material as Jim does on the square inch of material allowing for scrap. Most of my customers are other industrial shops. I can't mark steel up like you can for retail business. When I do 1 offs or a walk in I do mark material up x 1.43 That allows for 35% gross profit on material.
I charge for drafting time on custom work, repeat work I do not.
I use Mach3 so I do a simulated run to calculate time, add time for preheat & pierce (Oxy/Fuel) & on the heavier stuff I do (3/8" plate & thicker) I add an extra 20 minutes of time to load & clean off the table, carry scrap to the dumpster etc.
I'll leave it up to you on how much per minute to charge as rates vary greatly from geographic area to area. In my area I average about $400.00 per 8 hour shift for the table alone, not including material mark up etc.
I find myself in direct competition with the larger steel suppliers that run multiple head torches & tables as large as 8' X 40' I run about the same price per part as the big guys but my customers claim I maintain much better consistency to size & cut quality than they get from the big guys.
If it works.....Don't fix it!