The short answer to this is NO, you do not. If you pay for a tracking # on your package as indicated under the "Shipping" section of the project, you are paying for the tracking # or the whole package, not just one item. The same goes for the upgrade to a box for your shipment, the box will be for the whole shipment, so you only pay those upgrade costs once.
We want to keep this as cheap as possible for you and feel that is only fair.
The Limited Edition box will never be available through retailers or online or through distribution, we are only offering it through the KS project and then the remaining few copies through our website or directly at conventions later. It is just for you backers who want something special. If you prefer the other box then that is totally fine too, we will ask you for your preference for each copy of the game you pledge for in the survey that we send out. For example, if you back for 2 copies of the game and want one LE version and one standard version, that is totally ok. If you want 2 copies of one version, that is also fine.
There are other reasons to back this project, including a cheaper than MSRP price, very cheap or free shipping, and some cool stretch rewards, so we hope you'll stick around. But since you can get either box version on the project, not liking one version of the box over the other shouldn't deter you from helping us to make this game a reality. We do appreciate all of your support!
Yes, you can get as many packs of discounted gems for the game as you'd like, up to the number of copies of the game you backed for. If you back for 2 copies of the game, you can buy 2 packs of gems, but not 3. Yes these are discounted for backers, the retail price on the gems will be about $10. Yes you pay no shipping costs on these gems, they will come with your rewards.
Don't see the answer to your question? Ask the project creator directly.