Unable to run update_mysql in MySQL 5.5
As you  mentioned you are tying to run mysql_upgrade and it's looking for 'mysql.exe' and  'mysqlcheck.exe'.

Try this To make it easier to invoke MySQL programs, you can add the path name of the MySQL bin directory to your Windows system PATH environment variable:

Here is the link to set Mysql environment variable in Windows system path.

Hope this will help you.