Arch Pain

For several months now, when I get up in the morning the arch of my left foot has hurt enough that it makes me limp. The pain goes away when I put on shoes. Normally, these are running shoes since I run each morning. In what may be a related problem, if I go for an extensive hike (6-12 miles or so), the soles of both feet become painfully sore. Normally, this goes away very quickly after the hike. However, about a week ago I had the bright idea (so I thought) idea of replacing my hiking boot insoles with the Spenco insoles I’ve used for years in running and walking shoes. This turned out to be a big mistake – the soles of my feet were so sore after the hike I spent the evening limping and a week later the arch of my left foot still hurts.
I have very shallow arches – nearly flat feet, which I’ve always assumed was related to both of the above problems.Obviously, I exacerbated something by putting the Spencoe insoles into my hiking boots. However, do you have any suggestions for:1. What might be the cause of my morning arch pain and2. How I can avoid the pain to the entire soles of both feet when hiking?
I should add that I am otherwise in excellent physical condition. Thank you!