Change in behavior

I've had great success in further socializing Kira, but our dynamic has changed entirely. The first change, almost a month ago, we got new storm doors, and the one in back is now all glass and the kitties can see right inside. They were nervous for a few days, but now love watching us. A week later, I started getting Kira to let me pet her for treats. Once a night, then twice, four times, now she rubs on me every time I'm around. This is all going great, and Luna keeps watching and slowly coming closer. I know it'll be a while before she'd consider letting me touch her. But she's getting closer, and not as easily startled.

However, since Kira decided she enjoys being petted, she won't just relax and play in the garage anymore. We used to sit together, the three of us, for an hour. They'd play, groom, then sleep. Since I started petting Kira more, she won't stay in the garage. Only to be pet, eat treats, and sometimes she'll sit for a minute, but then she goes right outside the door and sits there. It honestly looks like she's guarding it. But Luna will stay inside, and sleep sometimes, or play. Once in a while, she'll join Kira in "guarding."

Am I making her uncomfortable? She purrs and leans into the petting, she rubs on my legs and arms. She'll sit in front of the back door for hours (apparently humans playing cards and nerdy games is fascinating to her). Luna will switch off with her too. She comes running to me every time I go out there. But I miss watching her sleep. I never force a pet on her, she sees my hand and I wait till she bumps her head into my hand before running it over her. I don't want her to mistrust me, and I've worked hard to make the garage a safe haven.

Now, I saw the other night, a mama cat with some kittens (playing in the road, no less!), but I believe another neighbor was trapping them. Gonna follow up on that. Tiger has been better, I haven't heard cat fighting in a long time. The construction has been going on for months, and I can't think of anything else that has changed. She's been staying in our yard much more. I'm not sure she even leaves it some days.

Anyone have any ideas on this? I'll stop petting her, but I don't know if that would make it worse. So far she's only let me and the other caretaker touch her. She won't even let my husband pet her. But she doesn't sleep by me anymore. Dunno what to think. 

It is interesting how things change from day to day. The doors may have done it, the cats may have had a tiff while you weren't there - hard to determine. But it sounds like you are doing all you can to maintain things.

I would explore the mom cat and kittens - just to make sure the situation doesn't get out of hand.