The way I look at it, she wouldn't have been wearing boots at 2:45 AM. Its a rustic cabin, so she could possibly have been wearing sneakers or comfortable footwear. I think she bay have grabbed the boots with the idea of running in to a marshy area, but for one reason or another didn't use them. Possibly she was caught, or she just felt she didn't have time to change them.
1:40a.m was the alleged cougar sighting while taking the dog out. So she might have still had the boots on from the walk. Also, here in Michigan, it's pretty cold even in Fall. Boots would be what most are wearing. Especially if she's a hunter and likes to be out. I don't see her bothering with sneakers. Also, if someone's shooting at you and you're panicked and shooting back, you aren't going to run and get a change of shoes IMO.
The gun was the same she used in the cabin to shoot out, the phone was the same phone she used to call the friend and I'm going to believe for now that the shoes were the same shoes she had on.