After doing a basic install of Windows 8, patch etc, I would like to be able to automate many post-install setup options/preferences and i'm wondering what the best approach to this would be.

For example, adding specific toolbars, resizing toolbar and buttons, folder options, etc... all the little things we tweak after we get our system setup.

The only thing that comes to mind now is to watch the registry with some software and see where the changes i make get recorded, my fear is that not all of them may be stored there...

Try Windows Easy Transfer. It's built in.
1) click Start
2) type "tr"
3) select Windows Easy Transfer
4) select 3rd option
5) select this is my old computer
6) select only your user account
7) click customize link
8) select only Windows settings (and program settings if you want those too)
9) click advanced
10) clear the checkboxes
11) click next
12) type password
13) select the save location of your .MIG file -- it will save the settings to a file you probably want to use a flash drive
14) rebuild your box
15) run Windows Easy Transfer again -- you should be able to figure it out from there

Do the community here a favor and write this up as a tutorial if it works for you as I've been strapped for time recently and always meant to do it!