After the game is loaded, kempston is highlighted. Therefore it goes without saying that if you press start the game will start using kempston joystick.

wrong. It Crashes due to no control method selected.

The fix pokes the value which is normally poked when you select "Kempston" from the menu. (65535,1)

The Kempston option also performs these strange IN A,(233) which is, I guess, something to do with the Gun Stick this game supports. These have been changed to standard kempston IN A,(31) commands.