when I try to run the MySQL Migration Toolkit GUI in Windows, I get an error that states Java is not installed. Java is installed, but Migration Toolkit doesn't recognize it. Does anybody know how to solve this problem?
You should really try the new Migration Wizard that comes with recent MySQL Workbench versions. The MySQL Migration Toolkit has been phased out several years ago and is not under active development.
For a tutorial on the Migration Wizard take a look at How-To: Guide to Database Migration from Microsoft SQL Server using MySQL Workbench.