In general, there shouldn't be any problems with Flash Player and Inventor. Error 1406 while installing is probably the most common issue with installing Inventor...here is Autodesk's page on solving the problem:
http://usa.autodesk.com/adsk/servlet...linkID=4183228
Mechanical Desktop should install along with Inventor. If you're having problems, you can install Inventor without Mechanical Desktop, and once Inventor is working, come back to the setup program any time and install Mechanical Desktop.