To quote the MDGX site:

The goal here is building the ultimate Windows 9x OS
by "transplanting" ~ 700 newer ME system files onto
98 SE, and YES, you too CAN do this at home, kids... :-)

The appearance is actually changed to look like Windows 2000
I don't personally like the ME version of Filemanager, much prefer
the W98 version with StepUp, Winzip and LFNs extensions, much better
than Explorer.

Someones also brought out USB drivers that are plug
and play like XP. And there's now a 98SE2XP project.

See http://www.mdgx.com/9s2m/ for SE info, there
is one for FE somewhere?

For the OP it might be easier to install 98SE on another
HD and then copy all the files over to your original HD.
I've done that before and deleted the original C:\Windows
dir first. I renamed C:\Program Files to C:\Program_Files_OLD
so that I would know what to install again. After installing
again I deleted the remnants from C:\Program_Files_OLD
If there are any huge files in C:\Program_Files_OLD delete
them and just leave the dir name so you know what was
there. i.e. C:\Program_Files_OLD\Pinnacle I did this because
I wanted full control over what was deleted on the HD and
all my files were intact. Obviously a backup Image needs to
be done first.

Sean B