Update:
Problem solved. My salivary gland was infected. Cured with a round of antibiotics
At this point I don't think it's my retainer anymore. I put my spare in an the pain is still there. Also I have stopped wearing my retainer as much. I take it out as soon as I wake up and only put it in right before I fall asleep. The only thing that seems to be helping is mouth wash and peroxide rinses. I'm calling a dentist today.
You said you had a tooth pulled in October and I said April...........sorry.
You had a tooth extracted back in April, but apparently had no pain wearing your retainer then. It seems the problem began after your puppy got hold of it and you bent it back into shape. Do you think there is a possibility you did more damage to it than the puppy?
The other issue is that you should be following your orthodontists rules to the letter about how often, and for how long, you wear the retainer.
I understand if you feel more comfortable with your own dentist, but wearing a retainer that does not fit correctly is undoing the work you and he spent years, and a great deal of money, correcting. I strongly advise you to make an appointment with your regular doctor as soon as possible. If you are going to be out of town for an extended period of time, find a reputable orthodontist and let him/her fix your retainer. And go ahead and cry if you must.......you will hardly be the first tears they've ever seen. And be sure in the future your puppy can't get to your retainer.