And I think that's' the best way to play this game.

You know sometimes the simplest explanation is the best one. I stopped fighting the controls and used them keyboard only and have come to terms with things. Not perfect, but certainly playable. Thanks for suggesting the one thing I did not consider

One other workaround is to play the Macintosh version. You can find it cheap, or on an abandonware site; or, if you're really patient, you can get it to work by combining the files from the Mac demo, the Mac version 1.2 patch and the DOS version. (The latter isn't recommended.)

I can't see what is the problem with the original controls. Just run the setup.exe with dosbox (or maybe there is a GOG tool for Windows for that?) and set the usual WASD controls. There aren't many places in the game where you even need to look up or down because of the autoaim system.