I finally dealt with this and now my unread email count is correct. I'm not sure which of the things i did was most effective but here they are:
1. deleted my pop account and reinstalled it -- this seemed to make it worse by increasing my unreads to 2500 from 326
2. went to my server and marked all my unread emails as read ( about 2500)
3. on my iPhone patiently and methodically marked all emails as read and deleted all the emails in my pop account -- using delete all
4. had set up an "all trash" folder earlier and kept emptying this as needed using delete all
5. repeated 3 and 4 as emails kept being downloaded to my phone but noticed that the number of unread emails kept decreasing
6. continued 3 and 4 until no emails were downloaded and all emails that I wanted on my phone were marked as read
7. tested with emails sent to myself using my computer
This was done several days ago -- after the update to 9.0.1 -- and all has been well since