My guess she has matured, and no longer accepts your right to crate her. You must not back down. The key to most behavior problems is approaching things using the dog's natural instincts. Dogs see all the people and dogs in the household as a pack with each having their own rank in the pack and a top dog. Life is much easier if the 2 legged pack members outrank the 4 legged ones. You can learn to play the role of top dog by reading some books or going to a good obedience class. A good obedience class or book is about you being top dog, not about rewarding standard commands with a treat. Start at
Raising Your Dog with the Monks of New Skete For more on being top dog, see
Establishing and Keeping Alpha Position
A wire grid in the bottom of the crate will help keep the puppy up out of urine and to a lessor extent stools. They are available with the crates, but expensive and hard to find. A piece of closely spaced wire closet shelving from a home supply place is cheaper. This reduces the mess, making the protest much less effective. The longer haired the puppy, the higher it needs to be. In warmer weather, you can just haul the crate out and hose everything off. When the puppy sees you coping with the situation, and you stand your ground, most of them give up and learn to relax, and that you will return. One more thing that may help is using a smaller crate, or blocking off part of a larger one so the puppy can't fouled one spot and retreat.
The "shut the puppy in a safe room" is a fallacy. Very few houses even have a
Safe room. How many of us have a room with a hard surfaced floor and nothing
Else? Most rooms have electrical cords to chew if nothing else. In addition
To destroying anything a bored puppy finds to chew, it may choke or have
Intestinal blockage from the pieces. I had a friend that left her dog in a
"safe" room. It ate a hole in the floor covering. The safe rooms fail to
Give the dog the comfort of the enclosed space their instinct requires. Nor
Do they restrict activity extending the time the dog can go without relieving
Itself.
I have never had much luck with the old clock or radio tricks with a new puppy. What I do is lay down by the crate like I was going to sleep there. Usually a puppy may fuss a little, but then settle down and go to sleep. Once it is asleep, you can get up and go to bed. This could help with your problem too.
You can also try the Kong with peanut butter in it trick too. It will last even longer if frozen.