Yep, your ipm is vveerryy slow. My first diy cnc ran 1/4 20 screws. I literally swapped 'em out 5 minutes in. Now I get around 30 ipm running 3/8"-16 (which is still way to fine of thread and pretty slow). .04" pass could be fine, all depends on the rigidity of your machine, run it as deep and as fast as possible before you get bad looking cuts or chatter (vibrations) throughout your machine.