Hey Carly,
First thing, keep in mind that you can't watch everywhere all at once. Jack may very well be coming back to Angel but using the TR site as his base of operations - perhaps because he has better lines of sight from there. And if he's close enough to be involved with both females then he is close enough to know what is going on at both sites. I had a male at the Radisson that I almost never saw - for two years. Freaked me out. And the first year T-Rex arrived, he actually used to crawl under tiny overhangs (he was small) when he needed a break, he'd crawl under and go to sleep knowing no one could spot him, I found him one day, purely by chance, and an extraordinary one at that!
And the territorial defense you saw, that's pretty standard. Since Milton isn't all hopped up on hormones right now, it could be that he was reticient to get himself in to deep since it sounds like Jack was in a 'roid rage at the time. And yes, females will join in on the chase though actual fights tend to be gender-specific.
Milton, hmm molting. Molting won't make him look like a juvie. Not in a million years. And peregrines like all birds of prey don't lose enough feathers at one time to imperil their ability to fly or hunt or anything else, they lose a feather at a time. The "spin-cycle" look you saw on the bird, when they've had a set-to, with humans or anything else, its very usual for them to puff up like that when they come to roost. It can be a quick way of seeing how stressed/harrassed a bird is after a visit, watch and see how long it takes them to flatten out their feathers so they look sleek again or until they start preening.
Would Angel be chupping at Milton? Guess it depends on whether she recognizes him as the mate she wants to be with. If Jack is decreasing his visits to her, she may very well be happy to see Milton if he starts to slip into his "provider" role. T-Rex took over a clutch of his father's in mid-incubation so I know for sure that its possible. Why would she fly after him but chup at him on the nest. One theory (note the word theory, I just don't know your birds well enough to say for sure) could be that when he's being chased by Jack, she joins in to protect the site. When he's sitting quietly outside the box and Jack isn't there protesting, she might recognize him as not a threat. Just a theory though.
Hope some of this helps ... even if it only gives you more things to look out for ...
