I think I can give some pretty insight on this as I have been in the Army for the past twelve and am currently in Special Operations.
Personally I think you would be fine to use the three day or even the four template. I would recommend doing your squats and deadlift toward the end of the week just to save your lower back. for example-
This way your lower back and legs will be fine throughout the week. I also would recommend using bodyweight for a few cycles as assistance just because I kind of over did when first started using 5/3/1. I will say that I believe this is thee best program for us as it consistently build strength over time. You just have to play with the assistance to hit your individual goals