An update on my situation:
Finally convincing my wife to have a massive blood panel was a godsend for us both. Her company has its own doctor that will run tests for free and I literally ordered everything I could think of and we got the results back on Monday of last week. The tests/doctor(s) explained a lot.
Estradiol -- (E2 or "Estrogen") <5. Almost non-existent. Absolutely soul crushingly low.
Progesterone -- <1. Again, almost non-existent and critically low.
Total Testosterone -- 7.3. Very low.
Free Testosterone -- .40. Very low.
Free T4 -- forget the number, but low
Free T3 -- again, forget the number but low
RT3 -- 17.3. I remember this because it was important in determining what therapy she needed. Anyway, it's too high and was blocking some of her uptake of T3.
She also had heavy thyroid antibodies present strongly suggesting that she has Hashimoto's.
Any single one of these markers is enough to make a person feel like complete shit, but her entire hormonal system was in complete shambles. I have no idea how long my wife has been in that state, but the doctor said it had likely been a slow degradation over years (which lines up with my experiences with her) and that her having been on hormonal birth control continously from 16 to now (more than 20 years) likely had a lot to do with many of her issues. The same day I had my wife go in for the tests I also convinced her to stop taking her birth control (as I have suspected it for awhile). Stopping the BC coupled with 25 mcg of T3 every day is already working wonders for her. I'm seeing a marked change in her behavior, energy, attitude, sexuality in just a couple weeks. She's coming alive again and I feel like the biggest asshole on the planet.
I have gained an exponential level of respect and admiration for my wife because I have no idea how she managed to get up every day to forge a successful career, maintain our home, and still have sex with me regularly while feeling like a zombie. I'm also amazed that she managed to avoid getting fat. It boggles my mind. We lead very healthy lives, but nearly every card in the deck was stacked against her. Now, I realize that she was giving me everything she had. She enjoyed intimacy with me, but she didn't have the energy, hormonal drive, or head-space to be flirty, sexy, or creative. I spoke with the doctor privately for more than an hour and he was astonished that we still have sex, much less as often as we do. He said that women with those numbers very often have completely dead bedrooms.
We're going to give it a few more months to see if her body continues to re-balance her E2, Progesterone, and Testosterone before putting her on further hormonal therapy. Things are slowly improving and after these revelations I just want her to get well.