Here are my first dozen questions:

1.  Best tax rate after Newbie Peas Mode but not having a bit standing army?

2) Change your tax rate to 0%. You need taxes to generate gold. You need gold to make units and support those units. As a newbie, you will NOT be making units for a while yet. Taxes to generate gold reduce your production of basic resources (wood, clay, iron, stone, and food). Early on, these basic resources are much more important to you than gold is. As you grow and start building units, you will need to raise your tax rate.

2.  Is there a way to defend vs Thieves?  (instead of reacting after I've been burgled)

10) Most likely, a new player will suffer attacks from Diplomatic units before armies. Diplos are anonymous, armies identify the attacker. You will defend against enemy Diplos with first, your Killing Rune. Second, by building your own force of Diplos. Your Diplos can stop enemy Diplos. But your defending force needs to be about 50% the size of the attacking force to be effective. Also, only Diplos of the same type stop enemy Diplos (ie, only thieves stop thieves, only scouts stop scouts, etc). You will build Diplos in your Consulate. Also, a low level vault is helpful to preserve a small amount of books and other advanced goods from thieves. If thieves strike, they will deplete your rune, and you will need books to cast a fresh rune. So, the vault could save a few books so that you can re-cast your rune without having to wait for new books to be made.

This is an excellent guide on self-defense for newbs: 
http://forum.illyriad.co.uk/basic-self-defense-for-new-players_topic2368.html

3.  Value of the Vault...does it defend enough resources to be worth the effort?

See response to #2

4.  When should I start researching Sovereignty stuff?

The absence of providing guidance to newbies in my guide is a clear indication that Sovereignty is not a game element relevant to a newbie.

5.  If a tree falls in the forest and my wife is nowhere around, am I still wrong?

6.  Best quantity of scouts and diplomats at the one week mark?

7.  Is harvesting resources near another person's city cause for an offense in this community?

9) Marketplace. You need a Marketplace to make caravans. You need caravans to ship goods to friendly cities, make trades in the Global Market, and Harvest Resources that spawn on the Map. See the separate topic here on Harvesting.

From the separate topic: When your van is interrupted this is called "bumping." This is annoying to many players but it is a common occurrence. I recommend not letting this irritate you. It is a widely-held view that van bumping is a-ok and some players even find it fun to bump each other. I do.

Killing vans, however, is widely considered an act of war.  So I recommend that you not do this.

Some players think they should send an army to guard a resource site and prevent other players from harvesting it. I consider this being selfish. Some players will try to destroy armies guarding resources.

8.  Does bumping occur most often when two people just try for the same resource at the same time?

See above.

9.  Why does my wife say "dammit Mike" when i dance like MC Hammer in mah big pants?

10.  From your experience, is the Architect Office even worth being built at all? 

5) ***The new building Architect's Office is best deferred by new players. You might want this building later, but it will not make a significant benefit early on. It's probably best to wait until your pop is around 400-500 to start this building. A level 10 will earn you a 15% decrease in build times for buildings. But it has an hourly food maintenance cost of 113/hr. Also, it requires almost 17K each basic resource to build this to level 10. However, if you are a player that has an empty building queue frequently OR if you use Prestige to speed build, then I recommend NOT building this improvement.

11.  Have any of you conquered an NPC city and was it worth the effort?

12.  Can you level up your commanders against NPC armies/cities?