Whether or not you try MyJEMM again, the error messages you’ve been getting are known problems, and most of what follows is EA’s recommendations:
For Win98’s MS-DOS Mode, you should probably be using the first config.sys setup that Starkey suggested (though you don’t really need to specify that much RAM–I use 7168, and less will work fine too.) In any event, I don’t think you should be trying to load your “files” and “buffers” high (as I note you’re doing in your original files); bring them back down to earth and try 40 again. If that doesn’t work, increase them to 50 (which is what I ultimately had to do on my Win98SE machine to get Privateer to run in DOS Mode).
If the game still doesn’t run, then instead of DOS Mode, use your boot disk with the same config.sys setup as above. If that doesn’t work, then delete the game, including the “Privater” directory, and reinstall on your C-drive using the boot disk. During the installation routine, configure the game for no sound or music. If the game finally runs after this, run the install program again just to configure your sound hardware.