I went to Apple store and consultant re-stored the phone to "new phone" again using a little more complicated method that apparently clears the firmware which the regular methods don't. He suggested I try it out for a couple of days and if it didn't fix the problem to come back and he made an appointment for the Genius Bar. I could tell almost immediately the re-store hadn't helped - the batterey dropped 5% in the 15 minutes I was in the store. When I got home I did another re-store and this time used my saved data from iTunes figuring why re-enter all the data for my mail etc if I was going to have to go back to the Genius Bar anyway.
No apparent reason why but this resolved the problem. The battery now declines 2-3% per hour - about where it was before I installed ios9.1. All the other little problems appear to be gone as well. Just restoring the phone 5 times may be the lucky number - it was for me.
I won't be putting the new ios update on the phone.