You have multiple issues and opportunities here.
Mail, Favorites, and other system settings.
Installed software and settings.
System files required by the installed software.
It's not simple or easy.
Personally, I suggest that the safest and easiest next step would be to re-install the applications you desire.
What is in the Windows 98SE folder?
This is not a "normal" folder on any system I have worked on.
Is this just a copy of the Windows 98 CD?
If the Windows 98se folder is where Windows was installed, you have a lot of work ahead.
In order to make things work without re-installing your applications requires a lot of knowledge about the programs.
First, you need to identify what if any programs need system files added to the Windows folders, and then copy these files and "register" them in the registry.
Next, you can simply move any folders in ProgrOLD that are not in Program Files to the Program Files folder.
Then, you need to add the registry keys for each software package.
As I stated, it is easier to re-install your application software rather than attempt to patch the registry to make it work.
Chas