Sounds like you are right on the line, and it could be easy to tip over into too much in the coming weeks. But at the same time, you could see some huge adaptations in the coming weeks as well.
1. This one is pretty normal for me. I do my runs first thing in the morning, and getting out of bed I always have to tell myself this is just going to be an easy, go by feel run. And it does take me a bit to get going, but 5-10 minutes in my system is feeling quite a bit better.
2. Like you, my legs take a lot more time to get going after a big session. I feel like I've done it right if they're coming around after 30 to 40 minutes. But sometimes they feel bad for the whole hour. How slow are you doing these runs? Mine are usually 75-90 seconds per mile slower than MP. But I often think of slowing them down when I see faster guys I follow doing them 2+ minutes slower.
3. Again, I think this one is fairly normal. But I might consider slowing those 45 minutes up even more. I don't know what kind of paces you're running, but my first mile is often over 9 minute pace and I just let the pace come down however it will after that.
I don't know what kind of program you're following. But sometimes I will take a whole week to run nothing but easy, cruising miles. I never feel like I lose anything after a week like this. I'm often able to add more miles and I come out of it feeling great and excited to get back to some harder sessions.