If all your devices have the same device type they will all use the same json file - whatever you put in the individual D_XXXX.xml files. It is usually the last one loaded during a restart but can be unpredictable. If you want them to have different json files, you will need to make them different device types.
The moment you changed the device file, it was no longer a standard urn:schemas-micasaverde-com:device:IrDevice:1 device so you should change this to a custom device type. It is good practice to use your own url rather than borrow MCVs for your custom devices.
Ok. And I can call it whatever I want for device type?
Well almost. Follow the same structure as existing device types. The url does not have to actually exist but it should be unique. You could use something like [i]urn:schemas-ramiasplugins-com:device:Screen:1[/i]
Would I put the same thing in the D_.xml file and the D_.json file?
The only penalty for inventing your own device types comes if you want to use remote apps. You may need to persuade the app’s author to include support for your custom device type. This will be much easier if you have used the same service ID, actions and variable names as the original device type.