I am no behavourist but I think that Haney
, is treating Indy as a burglar on his patch. He knows while she is in the cage his territory is safe and if he watches her she isnt going anywhere. As soon as she is out of the cage, well she is the enemy and to be seen off.
I think keeping them seperate is a good idea for now but think you will need to be a bit more proactive in a week or so.
Haney knows who indy is and doesnt like the intruder much, but she needs to get her scent round the house too, so maybe while Haney is shut in another room you can get Indy to come into the house in safety and let her explore. While she is doing this her scent will get distributed round the house and then when she goes back to her garage and Haney comes out again , he will smell her around the house.
As long as this causes no probs with haney then you are on the right track.
I would do all of this very slowly over weeks rather than days and if both cats are acting normally around the house, although not meeting , the next step will be to let them meet in the same room but I would wait at least two weeks until you try this, longer if one or the other is causing probs in the house due to the new scent.
I have four cats, two pairs and the two pairs do not really get on, its a domination thing cos one from each pair wants to be the top cat and the second pair to arrive are brothers and always looked after each other. One of them really fancies the girl cat from the other pair but she is semi feral and hates him. If she runs, he will chase her and I have had to stop fisty cuffs beteewn the four at times. I banish the birmans to a place where they love if it gets too bad, the bedroom lol.
However they have all been here for nearly 4 years now,,,,,,,,,,,,gosh 4 years or is it 3 LOL, anyway they tolerate each other most of the time and that is probably what will happen we Indy and the other two. Just prepare to be patient.