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Two part question:

Can you use spikey bits and have a master-crafter weapon?  Can you then wield two master crafter weapons and have spikey bits giving you 3 rerolled misses per turn?

Yes and no. While you can use spikey bitz along with master-crafted weapons, you only use the special rules for one weapon at a time. If you have two master-crafted weapons (which is only possible with the Imperial Guard) you would declare which is your 'primary' weapon and use it's rules while the second only provides an additional +1 Attack in close combat.

Also read page 5 of the Warhammer 40,000 4th edition rulebook under the heading 'Re-Rolls'.

I do not recall spikey bits being applied to a weapon, it is just a piece of wargear and have always seen it played:

AC with mutation 4 attacks, MC Powerfist and a Powersword.

4 attacks, up to two seperate attacks may be rerolled with Powerfist. As Ghaz noted you may not reroll a reroll, so you only get two rerolls if you miss on two of the first 3 rolls. works better with models with more attacks.
 
So against another WS4  4 rolls, two miss, reroll those two attacks once each. If you hit 3 of the first 4 you only get one total reroll for that one miss.

4 attacks, only one attack may be rerolled with Powersword.

So against another WS4 4 rolls 2 misses only reroll one attack once.

Ok makes sense. I should have thought about "only one special weapon can be in play at once."

Eh it was 1 am and was writing an army list and stumbled upon it. . 

just as a fast note,SB are only used in close combat also,not for firing weapons.