Hi there,
2003 is "can't connect to MySQL server" right?
I don't think that just restoring the files did the magic - if you didn't previously delete them in the first place :-)
desktop.err is error log (your computer is called "desktop")
desktop.pid is socket number where MySQL is connected to (normally you shouldn't touch this file, restarting MySQL is better)
Did you try restarting the MySQL server when you got the 2003 error?
net stop MySQL
net start MySQL
(from Windows command line; or using Services console)
When you try starting the MySQL server and it won't start, have a look into the error file desktop.err it should tell you why. If there's nothing there then the problem might be Windows related in which case take a look into Windows Event Viewer / Applications.
I hope you kept the original desktop.err before you overwrote it with the backup copy. If you didn't then well, we're talking just academically here. ;-)
P.S.: This thread should be better off in Databases forum, not PHP. But let's finish it when we're here.