To answer your question...there is no problem with manually removing software registry entries that you are sure are history.
I occasionally do this, although I don't make it a habit because I don't think it's that important to do this sort of elimination.
Most software will simply overwrite any existing registry entries, in the same way that files with the same name will overwrite other files that already exist when moved to that folder.
Occasionally, you run into a program where it's essential to remove all previous traces...to get an install that works properly (Symantec programs come to mind) but this is not normal.
Some links which may be useful/educational (what's more useful than learning?):
Backing Up and Restoring the Windows XP Registry - http://www.theeldergeek.com/windows_xp_registry.htm
Beginners Guides The Registry Backups, Repairs, and Protection - PCSTATS.com - http://www.pcstats.com/articleview.cfm?art...=263&page=4
Demystifying the Windows Registry - http://www.bleepingcomputer.com/tutorials/...l74.html#backup
ERUNT Registry Backup Tool - http://www.snapfiles.com/get/erunt.html
How to back up, edit, and restore the registry in Windows XP and Windows Server 2003 - http://support.microsoft.com/kb/322756
How to backup the Windows XP Registry - http://windowsxp.mvps.org/registry.htm