I worked it out in the end but cheers for your help. Neat mouse wasn't smooth enough with the cursor movement so I tried mousefighter instead and that worked a treat. Just had to write an ahk script to launch it and activate it straight away, then add it as an additional app to run on launch of certain games. I can now play Sega model 2 light gun games with the model 2 emulator using my joystick.
I'm trying to get my cabinet working so I don't have to press different keys to activate things in certain games, I just want to be able to press play, have the game load up and all the controls just work.