Hello,

A couple quick answers, and a comment.

1)  The Military uses Commercial Transportation costing, as often Commercial tranportation is used by the Military.  So the default values would be commercial transportation costs even if the Military is performing the transit.

2) I would recommend MIL-HDBK-1390 LORA.  I believe it is undergoing a Revision currently.  You can contact the lead of the revision at the Logistics Data Analysis Center (LDAC) Nathan Forbes @  nathan.g.forbes2.civ@army.mil  to possibly get a draft of the revised handbook, I'm sure his team would welcome feedback and input to that revision. 

And finally a comment.  Almost without exception, most LORAs are done as Non-Economic LORAs.  Simply due to the multitudes of "Constraints" required for a system.   I would recommend that the first baseline be an Economic LORA just to understand what each of the Non-Economic factors are costing (+/-) , then as you add each constraint/Factor rerun the LORA to see the impacts of each constraint/factor.  I know this may seem tedious, and unnecessary to run and re-run LORAs, but it will give you insights as to the true cost of each constraint/factor.