You've hit a roadblock that almost all WS hit. Something which should have been told, wasn't, and when it comes out later...bam! Back to square one.
You now realize that "protecting" her from the truth is only going to backfire. So, you've learned one of the hardest truths about rebuilding a marriage. The time for protection has passed, that time came around before the affair began...when you didn't protect then...you should NOT try to protect later.
If there is ANYTHING else which hasn't come forth...Tell her as soon as you get back home. I can't imagine how anyone can do true rebuilding while long-distance. jmho
IF at all possible, see if she will agree to just wait until you'll be back home where the two of you can work together, in person, face to face. It's so easy to miscommunicate even when face to face, it's almost impossible to communicate well long distance. You'll be home within two weeks...hopefully she'll agree to put things on hold until you're home.
When you do get home....sit down and answer ALL of her questions as honestly and completely as possible...but with kindness. (ie...yes, we were at "X" hotel...no...we broke the bed) If she asks a question which you need to reflect on...tell her to give you a little time on it.
You want to give a complete and honest answer, not one off the top of your head...which often can get you into deeper trouble. Take breaks! But set a time to come back and discuss it again. If one of you get's too emotional, have an agreement before sitting down that either of you can call a break, but you must set a time to resume...before breaking off.
A BS doesn't take one step on their healing path until they FEEL they are getting the truth. While it can be very difficult to hear the truth, we must feel that we are getting it.
Now, this may mean that you're being truthful...and she isn't buying it. This is normal, especially since she feels that you've continued to lie after d-day. It's up to you to be consistent in your answers, to allow her to check the sky if you've said it's blue. Understand that she must FEEL that you're doing your part, not only that you must do your part.
As for the put downs she is doing to herself, this is a self-esteem issue which isn't unusual either. She's had a very hard hit to her self-esteem and it may take a while to rebuild this. Continue telling her exactly what you said here...that she's beautiful, faithful, gentle, kind, caring, loving, etc. That what happened while it hurt her terribly, it wasn't for any fault in her...but was a fault in you. One which you will fix and make sure never happens again.
Good Luck!