1 and 3. So far I have decided not to use the SH3 Commander process to give awards or promotions to my crew, preferring to dole them out more sparingly as the game grants them. However, I did use it to grant a few of my crew some qualifications when I switched over to using the NYGM crew mod, since the posts I saw made it sound like things wouldn't work very well without qualified crew and since I was only on my 6th patrol I only had 1 or 2 warrant officers with qualifications. Since using the NYGM mod for the last patrol and a half, I've about concluded I really didn't need to do that. I also used the SH3 Commander process to give qualifications to several of my seamen - that doesn't affect the fatigue model but lets me easily determine which seamen I want to use for my bridge watch and my engine room and control room crew shifts when I set up my 2-shift alternating watch arrangements. While I'm still testing the NYGM mod out, so far I'm liking both the way the crew fatigues and the way they can (unlike the RUB model) regenerate, and I've just about gotten the hang of creating a workable 2-shift, 12-hour watch schedule.
2. I have set SH3 Commander to do crew transfers, but so far have only lost maybe a couple of crewmen to transfers (in 7 patrols). Generally (in my other careers), I have been manually transferring/releasing my then-most senior officer about every 6 or so patrols, figuring it was about time for him to get his own boat by that time. I usually just replace him with one of the free officers - it doesn't eat up renown and also gives me a chance to keep grooming up the more junior officers instead of ending up with a totally ace officer corps of equal rank to my own.
4. I've never gotten to the point of fully loading up all my officers with 3 qualifications, so I haven't experienced this behavior.
Good luck and good hunting!
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