1) No you didn't do anything wrong. In my original post it explains that the "Recent" programs list will only show icons for programs listed in the actual "Programs" folder, not the new subfolders (along with an explanation why I opted to take advantage of that fact).
2) The calendar on the Manila Home page is already linked to the Windows Mobile Calendar app out of the box, and it is not changed in any way by my cleanup. Therefore, any appointments you sync to the phone via ActiveSync (physical connection or over-the-air with an Exchange account) will appear on the home page automatically.