I would write the later two sentences as
I just now saw your call
I only now saw your call
They are very similar, but there are a few different nuances that I'd pick up on as a native speaker. One is that "just now" is best used to describe a single event, while "only now" can be used to describe a more gradual change.
Unions are only now moving towards implementing more progressive
policies towards transgender persons in collective bargaining.
In this case, the author isn't talking about one single event where unions suddenly took up the issue of transgender rights, but a more gradual emphasis in modern times.
"Only now" can also add a negative connotation to a sentence, in that it adds emphasis to the fact you didn't do this previously. For example, consider the following:
The President just now declared the opioid crisis a national health
The President only now declared the opioid crisis a
national health emergency.
The second of these sentences adds a negative connotation to the President's actions; it implies the author feels this is something that should have been done a long time ago, which the President is finally getting around to doing.
In your specific case, I would prefer "I just now saw your call" unless you let so much time pass before checking your missed calls that you really should have been expected to do it sooner, where "I only now saw your call" might be appropriate.