I have answers to most of your questions:
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You will neither be able to trade Garrison Resources (assuming you mean between players) nor buy/sell them on the AH, they are a currency and, as such, stored in your Currency tab. Also, it is of note that there is a cap of 10,000. Now, you can exchange other resources for Garrison Resources - change ore into them but not sure if you can do the opposite (change resources into ore.)
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I'm not following you on the 'trading' part of your question, but you can activate/deactivate as you deem necessary. Also, you can send any follower out on any mission that you have but their chance of success is significantly influenced by their individual skill set, Level, and iLevel. As for your specific example, again, I'm not following you. You get JC-based Work Orders when you build the Gem Boutique, and when you build the Gem Boutique you'll get Work Orders and Works Orders are different than Missions. Work Orders are essentially crafting orders that are completed in your Garrison that generate crafting materials and Missions are tasks you send your Followers to do 'outside' of your Garrison that generate Garrison Resources. Now at Level 2 or 3, you can assign a Follower to a crafting building, which will increase/enhance the yield you received from Work Orders.
For example, you mentioned Alchemy Lab, if you assign a Follower to the Alch Lab 2, you will get an additional daily quest for potions. And if you assign a follower to the Herb Garden 2, you get to choose the type of herbs that grow, otherwise, you are subject to the RNG, similar to MOP Farmville.
TL;DR
Crafting Buildings = Work Orders = Completed at Building = Generates profession-specific crafting material based on building type (higher yield if you actual know profession and/or have follower assigned).
Barracks = Missions = Completed outside of Garrison = Generates Garrison Resources, Follower Gear, Vanity Items, etc.
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Followers that you can take with you out into the world are limited to the 'Bodyguard' types and you can only take one at a time. I have not seen/heard of being able to take your follower into someone else's Garrison. And not sure you'll need to. I am assuming attacks on your Garrison will be more interrupts to production rather than the culling of your followers and NPC's by killing them or destroying buildings. I have not read/seen a lot on this particular mechanic but doubt Blizz would allow your Garrison or its inhabitents to incur any significant negative impact as the result of an attack. Or scale any attack that 'requires' you to recruit friends to end. Now, I do know that you can invite friends to join you in your Garrison that can assist you in fending off an attack - but I think this just shorten the timeline of the event rather than impacting the success/failure of it.
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I really don't have any concerns to add... I have, for the first time in many expansions, the time and ability to read-up-on and research (not in a combat zone this time). I'm a pretty big fan of WoWhead, and in addition to the Calculator Tool found at: http://wod.wowhead.com/garrison-calc#AkQjIQI there is also a pretty extensive Guide on everything Garrison that can be found at: http://www.wowhead.com/news=241230/guide-to-garrisons-in-warlords-of-draenor-buildings-plots-followers-missions-and
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In a previous post, you mentioned "From what I can tell we'll be able to share resources with each other. -If- that is so... we should arrange to have all crafts covered early on."
First to address the semantics - Resources (i.e. Garrison Resources) are currency and not tradable. Crafting Regents are Trade Good and will continue to be tradable as they always have been. As for profession coverage - we will likely have that addressed through professions actually known buy Guild members, and Guild members will likely pick the associated building for their already known professions in order to access the epic items. Remember, profession buildings allow you to craft average level items from that profession when you don't know it, or provide access to epic items if you do. Odds are, between all the guild members that will be leveling through WOD, all professions will be covered.
Plus, with the limited number of plots, I doubt a player in a guild that has all professions covered, would build on their spare small plots anything other than the Salvage Yard and Storehouse. You get three small plots - if you have one crafting and one the gathering - your gathering is covered by the other buildings so you can have both. If you have two crafting, like me, then you have a small dilemma - and have to choose between the Salvage Yard or the Storehouse.
The real choice/coordination that could happen between guild members is the Medium plots - BARN, BARN, BARN... oh, and did I mention BARN? Level 3 Barn grants Savage Blood that is required for all Epic-quality crafted items.
