Welcome to the forum Kethry
I don't grow Zygos, but I do grow oncids.
With the zygos is seems to be a pretty commen problem as I've heard from others who grow these.
I don't believe there was much you can do about most of those spots.
Sorry I couldn't help - maybe someobe else can.
The oncids do get black spots, but they should be very small and NOT spreading - many of mine have spots from higher lighting. I've accepted oncids and their spots, some always seem to be there no matter what.
Your yellowing leaves maybe a sign of your bulbs becomming - 'back bulbs', they will in time become leafless - it's normal, leave them.