Safe Combinations
Knowing the safe combination is useless since Jack Walters needs to find the clue before the safe can be used. For all combinations, start rotating the dial clockwise to the first number, then proceed in the opposite direction to the next number. Change rotational direction upon reaching each number and the safe's door should open.

100% Completion
First of all, you can only get an A rank if you get 100% completion. To get 100% completion you need to pick up ALL the journal entries for ALL 3 categories:

Jack's Diary - 13 entries
General Evidence - 18 entries
Mythos Tomes - 6 entries

You also need to find the rifle in the Refinery (it's behind one of the reception office doors), save Ruth from the rafters, and make sure you keep enough sailors alive during the boat ambush. Keeping enough sailors alive isn't actually that difficult, you'll only pile up the casualties if you hide inside the ship like a coward.

You will also need to complete the game in under 3 1/2 hours, and make less than 30 manual saves. If you make less than 5 saves then you will get a bonus rank, but you can't get an A rank unless you have 100% completion. In other words, if you complete the game in less than 5 hours (equivalent to a B rank time), but make less than 5 saves then you can attain an A rank (providing you get 100%).