That all sounds great and I look forward to trying the updated missions on our server.
Two other suggestions, which perhaps you already have planned are:
1) consolidate all of the calls for initialization of arrays and SMGoMajor etc into an init.sqf.
Unless you mean combining all the SM's.sqf into one, I have moved the array of missions to the configuration instead of the array that used to be in the block of code you would add to your server_functions.sqf. The missions are executed by two timer scripts which are ran from the init, which allows both Major and Minor missions to run at the same time. All the SM scripts are also no longer immediately ran and then call a script that makes them wait at the beginning, instead the SM.sqf isn't launched until the timer calls it.
2) add two things to bodyclean.sqf :
Bodyclean has actually been replaced with a function that gets called when an AI is killed.
a) something to update humanity for AI Kills, perhaps with a user-configurable variable.
This has already been added to the current version that I'm working on.
b) code to strip bodies of loot if they were not killed by shots from a player (not sure where i got this originally but I found a link just now as shown below):
I already have it checking if the killer is a player since I can't add humanity to a car, so I can easily implement this. Just threw it together so I wouldn't forget later on.
https://github.com/SMVampire/DZMS-DayZMissionSystem/commit/5fd7e8914300bb8fae3156cc6e5f366616a1621c