There is nothing wrong with your water quality, filtration, aquascape, lighting or size of your tank. JD are naturally very shy cichlid. JD should never be kept as a wet pet and needs company of tankmates to feel secure. You kept a lone female for months and without companion of her kind, she felt insecure and hide. When you added a male months later, he is observing her behavior to guage his own security. Because she is skiddish, so is he.
I had a skiddish JD before that I had to approach the tank slowly or else he would jump up. He wouldn't come out to feed until I sat quietly or walked away. But after I moved him to another tank with a community of African cichlids, the smaller but boisterous Africans drew him out of hiding instantly.
If you raised both JD as juvenile at the same time or with other cichlid tankmates, they will not be shy. You gave them Danios as dither fish but it is still not enough to bring out her shyness as Danios don't challenge them. It may be difficult to change their behavior now as shyness can be contageous, unless you can completely change the environment and gave them a bunch of boisterous tankmates.