I think the boots and wrapping her tail would be fine. You might consider a fly mask to keep debris out of her eyes, and help keep the wind down. I don't think the boots will make her too hot, either. If you're really worried, you can always get her a "helmet." It loops through the halter and has holes for her ears. Of course, if she isn't used to it, it could do more harm than good, I just think they are hilarious. =P
I wouldn't use a fly-mask is it's an enclosed trailer. It makes it really hard for them to see in the dark.
I don't put anything on my horses when transporting, unless they are known to hurt themselves. I used to bandage when we floated two horses and one was my feriends mare as she used to kick the other horse, but apart from that, never do, and never had an injury. I figure they would get uncomfortable, what if the boots started itching and the couldn't move to itch?