1. Where's the Merovingian archive store? I found one in Moriah but that was Zion. = (
Merovingian archive store is near appollyon NE, and the machine one is near midian East.
2. Is the experience any different then regular missions? Less, more?
Most of the time, the experience is greater. There are a few, especially in the earlier chapters, that are less.
3. Do you have to be in that org. to activate the mission? Could a Merovingian player use a Zion token? If so, do archives effect reputation?
No, you don't have to be in the same org and they don't affect your reputation.
4. Is there anything gained at the end of completing an archive/ set of archives? Like a special item of some sort?
When you complete a set, say all 3 orgs chapter 1, you can go to a special collector and trade the tokens for a noninfectious flame virus. You can find them in different districts, and they're usually labeled "machine (or other org) collector. If you do all of one chapter for all 3 orgs, you can go to any collector and trade for whatever the reward is for that chapter. If you do chapters 5-8 for the machines, you'd have to go to a machine collector and can trade the tokens in for the top half of pace's agent suit. The collectors will show what tokens you need to get the items. I know there's a Merv one by Chelsea NC and I think there's a mach one near Mara C and a Zion collector near Camon C.