The check engine light keeps coming on after the code reader shows a pass code 111 for all the OBD tests. I did notice that the reader sees it as a 4 cyl and it's a 6 cyl, would this cause the light to go on?

What year please. If it is the early EECIV system, you may need to read the codes while the light is on. Some of the codes would not store on the early systems.

It's a 94, I have tried to run the diagnostics while the light comes on. I've noticed that when I do run the tests it clears a then when I run it normal it comes back on. I'm still wondering if its because it sees it as a 4 cyl?

Try this site and jump the connector as shown. Count the flashes or sweeps on the meter. A 111 will show up as flash flash flash. If it is EGR flash flash flash-pause-flash flash flash-pause flash flash. This equals a 332. Let me know if this helps.
http://www.troublecodes.net/Ford/