PubIt! is quirky and what you've experienced has been the norm for a while. Things sometimes proceed slowly and they are not always synchronized.
You should wait at least three days. Your covers will probably appear. Just give PubIt! more time.
As for the technical difficulties message, it's been appearing for at least the last three months. Sometimes it means nothing. You just have to keep checking at B&N to see if your ebooks are published and if your covers finally appear.
PubIt! claims it can take 72 hours so you shouldn't worry until at least three days have gone by. It is normal for your ebooks to indicate "in progress" until everything is finalized. Again, you have to be patient.
As for your author bio, yes it needs to be included each time. What I do is keep a copy in a simple text file that I can copy and paste as needed. That way I only had to type it once.
Kind regards, David