Calm down Deanna, all is not lost. I believe the ll to 12" is still around the center of the door (up and down) which is what you want for the best structural supporting in the door.
As far as the 6" above the knob and interferring with the storm door, well the deadbolt should only stick out about an inch or so on the outside of the door. Go outside (without locking yourself out) and eyeball it or the easy way is to measure from the edge of the door stop to the storm door latch to see if it clears which it should.
If the 11.5" is around the center of the door up and down I would put it there which is where you already punched it. But before drilling, check the predrilled jamb to make sure your jamb plate will fit and that the deadbolt fits the hole otherwise you may need to drill it bigger.
I'll be around for a few minutes yet if you have another question otherwise good luck and when I need to break in after you are done, I'll go to the back door. take care.