The tool was designed to assist in the migration, but it wont deal with every scenario. There is no easy way to upgrade a DOS app to a Win32 app.
If you just need something that just run, I would recommend going line by line thru the syntax errors and make sure you can atleast build an exe and then make sure it does what you need (drivers work, GUI is effective and so on). If there was any hardware interaction, you would probably need to find the 32 bit version of the drivers and deal with any API changes that might have happened over the last 15 years. We always try to avoid making API changes, but a change from DOS/Win16 to Win32 sometimes requires it.
If you want something that would work for the long run (XP, Vista, x64?), I would suggest evaluating the purpose of the application and see what it would take to create a Win32 app from scratch. Support for
Win98 and ME by Microsoft has already ended. If you would like to keep using the app for another 15 years, perhaps the work might be worth it.
Good luck with your project.
Bilal Durrani
NI