1) How do I change a shopkeeer's inventory? Where is his/her inventory stored in the CS?
If you open the NPC's properties (double-click on them), you'll see an inventory. This is usually the primary source of inventory items. However, shop keeper inventory comes from their own inventory and all items and containers they own in the world.
2) Every time I selected a shopkeeper, his/her info was greyed out and I couldn't edit the NPC. I recall this being a buffer to prevent glitches, conflicts, etc. How can I edit NPC's like this, and why exactly are they protected?
This usually just means the NPC is set to autocalc, which uses their class to automatically calculate what their skills and stats should be (with a level provided). To disable this, just uncheck autocalc in the NPC's properties screen.
If that doesn't work, the template may be locked; right-click in the NPC list and uncheck the lock option.
3) How do I tie an item ingame to a shopkeeper's inventory?
You need to give the shopkeeper NPC ownership of the item. This means either adding it to their inventory (drag and drop into that section of their properties window) or setting the ownership on the item/container. To do the latter, double-click the container, and in the owner/set owner section, pick the NPC's ID from the drop-down list.