Immunities/Resistance, Red Sign of Shudde M'ell and Equipment Timing
While generally it doesn't matter, all the dice in a skill checks should be rolled at the same time. So it doesn't matter which order you use various spells and items. (The only corner case I can think of at the moment is the Lucky Cigarette case, which lets you reroll all the dice that you had in the check normally in addition to any that were added to the check due to clue token expenditure, but that's not quite the same situation). It looks like your confusion is arising from your second scenario, in which you roll dice for the skill check as you select additional items to use. You should be looking at everything that's getting used in the battle (weapons, allies, environment, injuries, combat penalty, etc.), figure out the aggregate bonus/penalty, apply that to the base state (Fight, Lore, etc.), and then roll that many dice. So the order in which items are 'applied' is irrelevant.

So the correct scenario is this:

3) If you succeeded at casting Red Sign, the Witch no longer has Magical Resistance, so the Enchanted Knife gives it's full combat bonus of +3 (The +4 is the Enchanted Blade, not the Knife). Adding in your Fight score of (as an example) 3, the Witch's Combat modifier of -3, and (for further example) Tom 'Mountain' Murphy's bonus of +2, you end with a bonus of five, so you roll five dice. Everything gets summed up and everything gets rolled all at once.