Anyway, this is going on too long and it's time to leave work, so I'll leave it to someone else to explain how to use your computer.
Honestly, I don't see what your problem is, almost everything in your list is something I do every day without any of your issues.
Search is not only based on what is indexed, however to remain quick search will only initially check indexed files. You just click on "more results" if you don't find what you're looking for, and if necessary "my computer" and you will find the rest, but it will take a much longer time, so it's better to just index you drives if possible. Besides, you really shouldn't rely on search functions, instead just pay attention to where you put things, what will you do if your OS gets corrupted and you can no longer search? Also, if the files are hidden, or are in a hidden directory they will not show up unless you either unhide them, or change your folder options to view hidden files/folders.
You can still choose a specific location to search just by navigating to the folder you want to search and typing your search in the search box, that automatically limits the search to that folder. Once you've done that it's just a matter of sorting by whatever criteria you want, it's very easy.
As far as extended desktops go, just disable the extended desktop from your driver icon in the system tray, nearly all drivers support this, and bam, all the items and windows on the extended display will be snapped to the only remaining display. Cake.
There are other ways but this is the easiest, and really you shouldn't be storing stuff on your desktop, it's just a waste of your system resources, just pin commonly used things to the Taskbar, and once they are pinned you'll never need to look elsewhere for them. If the Taskbar is too small just unlock it and resize it, more space instantly.
As far as a list view in the control panel, just try out the views provided till you find it. It is there, and it shows everything in alphabetical order, really you just need to try things out a little, it's not hard.
Unlike, older versions of windows you can pin any program to the Taskbar. If you're really in and out of the start menu often enough to nitpick how "All Programs" is displayed, you're doing something wrong.