1. The decision to continue using MIL-S-13165 or AMS-S-13165 is a policy issue. Some organizations require continued usage of a updated, or cancelled, specification while others may require migration to the newer version. Be aware that AMS-S-13165 has been cancelled with re-direct to AMS 2430. You should ask your customer for specific instructions on which spec he expects you to comply to.
2. Increasing your orifice plate to 3/8" will increase the shot flow rate (substantially). This increase in shot flow rate will reduce the air pressure at the nozzle (not at the source) thus your intensity will drop unless you increase the air pressure, as you have done, from 50 psi up to 80 psi. I'm not clear why you would have changed your travel speed from 12 to 6 in/minute. This would affect coverage rate and since you are already throwing almost twice as much media per minute you shouldn't have had to change your travel speed.
Are you preparing complete saturation curves (four or more strips exposed at increaseing exposure times, or in your case decreasing inch/minute feedrate)? Are you really sure the media is within requirements (size, hardness, shape). What grade of Almen strips are you using?
