http://www.hyline.com/userdocs/library/Repiratory_Diseases.pdf
((reviews different respiratory conditions that can damage the reproductive tract)
http://www.filemanage.co.uk/pubs/Psittacine_birds.pdf
"(egg yolk peritonitis)...Therapy: Treatment depends on the severity of the clinical signs. Traditional medical management of chronic cases includes long-term parenteral antibiotics based on culture and sensitivity, and supportive care
as needed, including abdominocentesis to reduce abdominal pressure and relieve dyspnoea. The aetiological agent of egg-related peritonitis is often a coliform (usually Escherichia coli) but Yersinia pseudotuberculosis and
staphylococci have also been associated with this condition, and anaerobes and Chlamydophila have been implicated. ..."
http://www.merckvetmanual.com/mvm/index.jsp?cfile=htm/bc/205804.htm
(Egg yolk peritonitis)
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Egg peritonitis is characterized by fibrin or albumen-like material with a cooked appearance among the abdominal viscera.
It is a common cause of sporadic death in layers, but in some flocks may become the major cause of death and give the appearance of a contagious disease. It is diagnosed at necropsy. Peritonitis follows reverse movement of albumen and Escherichia coli bacteria from the oviduct into the abdomen.
If the incidence is high, culture should be done to differentiate between Pasteurella (fowl cholera) or Salmonella infection. When hens have too many large ovarian follicles, a problem described as erratic oviposition and defective egg syndrome (EODES) is seen in broiler breeders. This condition is accompanied by a high incidence of double-yolked eggs, prolapses of the oviduct,
internal ovulation, and/or internal laying that often results in egg peritonitis and mortality. EODES is prevented by
avoiding light stimulation of underweight pullets too early and following body weight and lighting recommendations for each breeder strain. Overweight hens may also have a higher incidence of erratic ovulations and mortality associated with egg peritonitis. "
Cyn, it is just my opinion and god knows I am no expert, but I do not think it has anything to do with "bad " genetics (too far inbreeding or such) but more to do with a combination of things (and as you yourself have said you have had a lot of different problems with this flock > a bird may recover but when you have problems of the sort you have had and you are unable to move them to a new area then the problems tend to stack up and more and more birds will be affected.
Personally I think there is little you can do for the current flock (overlighting may have played a role in the internal laying problem you are experiencing and they will either be affected by it or not) but I do feel moving your entire flock out of the current area you have them in and reviewing your light management (for future stock) as well as choosing a different type of substrate for their ranging (the problems with all the pododermitis/bumblefoot (staph) issues you have experienced) ... one that is dry and less shady (sun/UV light on ground will help control any organism overgrowth) will be helpful with future stock.
I also do not believe that organic/non-GMO feed is going to solve your issues either... however I do believe that nutrition feed and supplementation can help you. You will have to do a lot of reading and review your current feeding /supplementation regime to see if and to what extent this may have played a role in the problems you have been experiencing. The article above mention EODES and the information (nutritional) is mainly specific to broilers and here below are a few articles:
http://www.thepoultrysite.com/articles/357/breeder-nutrition-and-chick-quality
http://www.avian.uga.edu/documents/pip/2002/0302.pdf
and here is an interesting excerpt from the following article link:
http://www.canadianpoultrymag.com/content/view/962/38/
"...Backyard flocks would generally have used dual-purpose breeds, which had an adequate rate of lay but also had enough fleshing to make a good meal when needed. These flocks would not get larger than 200-300 birds due to problems controlling diseases like coccidiosis.
But with the introduction of high-energy feeds and linear programming for diet formulation (done by hand), the door was opened for the development of a specialized broiler industry.
Following less than 20 years later, the negative impact of selection for growth on the reproductive capabilities of the broiler parent-stock was becoming apparent. A 1972 study compared high and low juvenile body weight lines, and reported that the high weight lines produced more eggs than the low weight lines, while settable egg production was reduced. High weight line hens showed increased rates of internal ovulation and defective egg production (36 per cent vs. 2 per cent in high and low weight birds, respectively).
This relationship is typical of many full-fed broiler breeder hens, where there is difficulty adhering to the normal models of the ovulatory cycle. Studies on arrhythmic laying patterns in meat-type hens in the late 1960s and early 1970s led to the description of a condition called erratic oviposition and defective egg syndrome (EODES).
Hens affected by this syndrome often lay erratically throughout the entire day. A 1992 study reported that during the first few weeks of lay, hens that had been fed ad libitum from hatch laid 40.8 per cent of their eggs outside the normal laying period the first 10 hours after dawn signal. The laying of a defective egg can often be the result of an inappropriately timed ovulation, either bumping into or forcing out the previous egg early. A period of at least 21 hours before or after another ovulation is needed for the production of a normal egg...."
ETA: Sorry to hear about Rosemarie (((hugs)))
