All Missions/Ops Complete. Help with rounding out 100%

About to start my struggle to go through all the story missions and round out the Mission Objectives (none of which are destroying the anti-air radar, but it does put a hole in the enemies' air surveillance) to get closer to 100%.

To anyone who has succeeded at 100%ing I have to ask:

1. Do I need to do all tasks in a single run or can I just do the ones I have left unchecked from previous runs?

2. Do I need to finish on an S-Rank? My Phantom Limbs changed from S to A when I ran back to do the extra tasks, I'm worried I'll have to do that mission again now.

3. If S-Ranks are negated, is it preferable to use stealth/bandana/etc to get the objectives done and then round back later for S-Ranks?

4. Which missions will give me the biggest trouble? Extracting 7 vehicles in Mission 45 sounds impossible, especially without D-Walker's fulton launcher. What are the biggest obstacles between me and 100%? Are there tips/tricks/development options to start early so I don't get caught up?

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Thanks in advance for all who can help.