Poor mommy, I can see how this would frazzle anybody.
Kids go through normal stages of separation anxiety. With her daddy around less, it could be she's worried about you being around less, too. We often use the phrase that kids are "testing" limits. They are, of course, but not in the planned, thoughtful way a teen or adult might. They are just behaving in ways that come naturally, and virtually all behavior is grounded in some need they are trying to fill. And in the process, limits get tested, strengthened, or discarded.
I have two thoughts on helping her (and yourself). One is that you try emotion coaching. Google this for some really useful tips you can start applying right away. And/or look at this (and related) videos, in which Dr. Harvey Karp, author of The Happiest Toddler on the Block, demonstrates some good coaching in action: http://www.youtube.com/watch?v=fJ1428uYs2g&NR=1&f.... And add How to Talk So Kids Will Listen, and Listen So Kids Will Talk to your parenting library. You'll reach for this book again and again over many years when you discover how well it works.
My other suggestion is about supporting her health needs in new ways, which makes a measurable difference for some children. I have watched children fall apart emotionally during tests for chemical sensitivities, which I suffer from myself, and which can have a powerful impact on mood and emotion. Children who are peacefully coloring or reading can have a tiny squirt of some chemical under the tongue, and in minutes transform into a raging or weeping or impossibly stubborn barbarian. I have strong mood swings too, that are hard, even as an adult, to manage.
If you want to experiment with this possibility, try garbage-bagging household cleaners, air fresheners, fabric softeners, all scented products including your own toiletries for two weeks. Keep her exposure to auto exhaust, paint fumes, new plastics, dry cleaning, or any source of volatile chemicals as minimal as absolutely possible. (You can use baking soda or vinegar to clean almost anything.)
Also avoid processed foods that have any artificial colors or preservatives, both of which have been proven in a large study to aggravate behavioral problems in sensitive children. If you find she has an easier time, you have some useful new information. If there's no change, then resume using the bagged products (but be aware there are some nasty toxins in many common household products).
Finally, making sure her diet is well-balanced and nutritious is important, because a lack of some nutrients shows up in some children as behavioral problems. Consider adding Omega 3 oils (fish, flax, or walnut) to her diet if you don't already do this. A good balance of B vitamins can sometimes help, too.
I sure hope you find something that gives you both more space and calm.