It takes them a while to regulate. I don't know what your set up is like, but all my eggs have a thick shell. I have never had a chicken die from an egg breaking internally.
Hens over 2 years old are prone to reproductive disorders, those are normal. But, you have too many roosters. Have you ever thought about cutting down on them?
That sounds like the reason for deaths. Soft eggs are nasty. Egg shells are okay to feed, much better than bone meal IMO. I have been feeding it with no issues and no soft eggs, except 1 or 2 from new layers. But most of my layers are hens, so I havent gotten a soft egg in over a year. Last year...
My recommendation would be to make sure that they are in a stress free environment and provide them with egg shells (baked and crushed). The fact that some of your deaths had to do with eggs breaking, prolapse, my guess would be their eggs are too soft. Chickens definitely prefer egg shells over...
I actually own more chickens than you do...Sounds like you fed them really well, apart from slightly less protein. Its odd to me that they would have liver issues...
How much protein do you feed? Layer feed or All flock? Do you provide oyster shells on the side? I have had 5 losses in 6 years, more losses after I started free ranging.