ME-to-W2k is not a valid upgrade path, and results are usually
disastrous. ME was written after W2k, so the W2k installer doesn't know
how to interpret the ME settings and so forth. I would just start over
with a clean install of W2k on a freshly formatted partition.
If you decide to use the currently installed W2k, you can get rid of the
ME by doing 2 things:
(1) edit the C:\boot.ini file to remove the reference to ME. Boot.ini is
a very small hidden/readonly/system text file; to see/edit it you must
remove those 3 attributes. Start/Help/Reference/MSDOScommands will give
you the syntax of the attrib command.
(2) after making sure the system boots correctly to W2k with no boot
menu display, you can then simply delete the ME system directory and all
its subdirectories to free up that disk space. This step is not strictly
necessary (it can be handy to have a backup system) but that space may
be useful one day as W2k grows, which it probably will.