4.0. And the reason I installed it over NT instead of a clean boot (aside from simplicity) is that I already had NTFS and I didn't have any apps there weren't ready for 2000. I ran the compatibility check prior.
"Upgrading" over a previous install is nearly always a bad idea. 3rd party drivers can be "successfully" migrated but not really compatible; double check you have the newest W2K-certified drivers for all your hardware. Also, subtle registry errors can be pulled along as well--a million things can go wrong.
That said, did you install all the fixes available via Windows Update? Can you shut down successfully?
If so, it's probably a driver issue which is why it's important to get all those updates. Also, check the Advanced Power Management and try turning it off.