You may find these 2 items to be of interest:
http://www.vistax64.com/tutorials/211637-explorer32-shortcut-vista-64-bit.html?filter[11]=Shortcuts
http://www.codeproject.com/KB/system/ExplorerObjects.aspx
For Custom Explorer startup locations I've found it easiest just to make a shortcut and put it on a launch bar such as QuickLaunch or RocketDock.
I gave up on doing much with Start Menu customization. I tried to make a custom icon for my program's folder group in the start menu, and succeeded, but it would only take effect after the user logged off, then back on. Seeing the folder change probably would just make them think I introduced a bug into their system. I abandoned messing with that mess. I use RocketDock with a bunch of folders to group my shortcuts and zero desktop icons. Sorry, I rambled.

edit: the other one to check out would be google Explorer Command Line for switches such as "select" to customize how it comes up.