If you give more information, maybe we can help you better. I and several others here have GD working on Win98/PWS, so one of us ought to be able to help you.
First, you say you have updated the php.ini file but didn't give any details. You probably did it correctly, but just to make sure:
1) Did you change the extension_dir to C:\php4?
2) Did you uncomment extension=php_gd.dll in the Windows Extensions list?
3) If you have other extensions active, is php_gd.dll first on the list?
Share what code you are trying to execute and what behavior or error message(s) you observe. Otherwise it is tough to help.