Explorer is the shell ;)

But Explorer has had it's fair share of issues. I have a 98SE machine to prove the stalls, lockups, lack of refreshing directories, etc...

Not anymore, not entirely. Start menu and taskbar are now in a separate thing I believe. Welcome to 20s!

Explorer.exe is still the shell -- the shell is defined at HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon\Shell, if you want to look (or replace it).