Very iiiiinteresting...
Could you share the wiring diagram?
Positional guns are very easy to mod. Especially if you just buy an actual arcade gun off ebay. X should be AD0 and Y should be AD1. Then any buttons on the gun can just be wired to shot 1, etc.
From what I have seen, most light gun games that work on a JVS system will have the guns connected to an additional gun I/O that in turn plugs into the traditional JVS I/O. The gun I/O will decipher the coordinates of the light gun shot on the screen and then convert that into an analog signal that the I/O uses to tell the PCB where the shot should hit on screen in the game.
Most light gun games reload by shooting off screen. The game determines this signal in two ways based on the system you are using. Older systems would determine where the shot should land by using a photo optic sensor in tandem with the pixels on screen to read where the shot was aimed at a CRT monitor. Newer JVS based systems such as Naomi, Chihiro or Lindbergh were designed for use with sensor arrays. Sega began using them with model 3. Why? Not sure. Did they have the foresight to see the CRT become obsolete years before flat screens made their appearance in homes? Regardless of the reason, they are necessary to use a light gun with flat screen displays.
With the traditional CRT system, the game would send the signal to reload every time the photo optic determined that the shot was not aimed within the parameters of the screen. So the sensor array does this a bit different. The game predetermines the boundaries of your screen and assigns them their X/Y coordinates. If the coordinates of where you are aiming the gun falls outside of the predetermined boundaries of the screen when you pull the trigger, the gun I/O will then send a separate digital signal to the JVS I/O that will tell the game to reload. The digital input used for reload is usually different for each game. It will probably never be shot 1 since this is usually assigned to the trigger pull.
That is a long winded way of saying that if you use a positional gun for a light gun game you will most likely need to wire up a reload button. But it is cool because you can bypass the gun I/O completely if you are using a positional gun and still have fun playing the game with an experience that is mostly the same. Once you are in the game you really don't pay attention to what kind of gun you are using. I have used my S-JIHP pcb to play light gun games on many different systems. I have used it to play Confidential Mission on Naomi. I have used it to play Rambo, Primevi Hunt, and Ghost Squad on Lindbergh. As well as Virtua Cop 3 on Chihiro. All have worked fine. The only one that didn't require a reload button was Rambo but I think that is because it was designed to work with either type of gun.
PS---I am no electronic engineer. Some of this may be inaccurate. It is just how I have gleaned that the systems work from looking at schematics and playing around with the hardware.