RedBaron, lets get you started at least in filling in some of the blanks.
There are so many factors in your question it is hard to know where to start but here are a couple of points and hopefully others will add their 2CW.
Keep in mind that the higher your Z axis goes the greater the importance of building to insure that the Z axis is perfectly perpendicular to the table, if it is off at 1" height the error will multiply as it is raised.
The higher you go the more rigid the construction needs to be.
Depth of cut is the amount of material that is removed while cutting. I think you are referring to "Tool Length" which is something all CNC machines need to know prior to cutting, this is the distance from the tip of the cutter to the top of your part you are machining. I know from personal experience what it does when you overlook this step
You will have a great deal of trouble finding a 6" end mill in the sizes that will fit routers as the longer it is the larger the diameter it needs to be otherwise it will simply flex and break.
In reading so many of the post here at the CNCzone it seems that most Z axis heights are around 6" or so even less.
If I am using a 6" end mill, then the maximum depth of cut I could make is 4-5" for fear of the router hitting the work
While your terminology may be incorrect you are essentially correct, the length of the cutter itself, the tool holder size and how close the surrounding material's walls are to the above all play a role in how far the cutter can reach into your part.
Well here is a start for others to add to.
Hope it helps a little.