1. Is there a way to add new wound boxes to a character? Like giving each wing 5 wound boxes that are independent of the others?
Yes. The name of that power is Custom Hit Locations, and it's on p. 143 of the big book. (Not sure about the Essential Edition.) You might also want to consider the Extra Tough miracle, which will give you some extra wound boxes to spread around.
2. What extra's and flaws would be required to make a weapon that is so specific?
Here's the way to think about doing it: make it as effective as it needs to be for its most effective state, and then Flaw it down for the conditions where it's not as useful (in the universal sense of useful, not Useful, if you see what I mean).
The fact that sometimes it's a sword and sometimes a mace is an almost irrelevant detail as far as the mechanics are concerned. Those are just special effects.
Here's what I would do:
Holy Weapon 6d (A U, 5 per die, 30 points)
Attacks Extras and Flaws: Burn +2, If/Then -1 (Burn and Killing damage apply only to unrepentant murderers)
Useful Extras and Flaws: None.
You roll 6d to attack with this weapon; it does Width in Shock & Killing, plus a burn effect, against murderers. Against other opponents, it does Width in Shock.
The Useful quality is that by its very nature it detects a target's moral state, which (IMHO) is worth requiring you to spend points on. Your GM might disagree. I threw it in as an extra quality, and I would just have it work automatically if you hit. If you're into powergaming, you could buy it cheaper as a separate 2hd miracle (8 points vs. 12 -- better still make it Attached and Automatic, for a net 4 points), or even as a 1-point dud power, depending on the campaign.
Of course, the whole thing probably ought to be bought as a Focus, which will reduce the cost per die further. Don't forget that you can't reduce the cost of any single quality below 1/die, though.
Finally, you could also consider defining the Attack quality as Brawling Hyperskill. That would let you add your Body + Brawling to the dice roll... but that wouldn't allow you to use the Burn extra (unless you bought the Burn extra on your intrinsic Body + Brawling as well).
I hope that helps, and I didn't just confuse you further!