Like mentioned, all power-assist EB masters had the ports on the right, while manual masters had them on the left. I think you could special-order manual brakes even in the last couple of model years, but not sure if I've ever seen one first-hand.
Nobody brought it up yet, but in case you were wondering about it, I'm pretty sure that the master cylinder's piston bore was the same size for both power and non-power, disc and non-disc Early Broncos. So no problem there.
Reservoir size for the dual-reservior types was virtually the same for all years too.
Another "possible" difference is that the port for the front brakes on a manual master might have come with a residual pressure check valve behind the brass cone seat.
While I would think that all the original ones were so equipped, not all aftermarket ones have the valve. Either way though, you'd want to check, and if there is one, take it out for use with disc brakes.
I used mine for awhile that way, with no ill effects. However, the potential for dragging brakes is there, so I'd remove any RP check valves present.
Basically then, you'd usually end up using the master that was appropriate for your body (power or manual) and/or for whatever hoses you're using from the master cylinder to the frame.
Only needing to remove any check valves (disc side only) and make sure you plumb the front disc brakes to the rear (larger) reservoir's port.
A lot of us are running Ford disc brakes with the orginal masters with no assist. Works fine for me with up to 33" tires at least.
Good luck.
Paul