I guess I'm not really sure what my issue is, air leaks on start up and when spindle is turned on, also the tool changer stops in the up position every time I try to change a tool.
You can check the fittings on that Bijur, but a little air leaking on startup isn't a big deal. That Bijur looks like it is there to meter oil into the spindle air. My Haas does that too. Straight way oil on each axis, and oil/air injection at 6PSI to the spindle. I don't know what's normal for Fadal, but in general, it's not unusual to see that kind of arrangement.
It's not uncommon for spindles to use air when they are running. Some machines use more than others. My Chevalier spindle exhales for about 30 seconds after M30.
That filter is just a filter only- it doesn't regulate the pressure. If there is no other regulator where the air comes into the machine, it's getting the 100psi that your compressor is putting out. Most mills will have a filter regulator and (sometimes) lubricator where the air comes in.
It's not a good idea to have unfiltered, unregulated air to the machine. If you don't have a filter regulator now, you should put one on.
The tool changer is another issue. If you want help with that you're going to need to provide more information. Year and model of machine, type of tool changer, exact behavior, alarms, etc. I'm not a Fadal guy, but there are several knowledgeable Fadal people here that will help you.