Hi Daniel,
I am one of the two people that started this discussion. I also did my NE presentation on Healthy Eating on a Budget. My degree is in Economics and I work actively on our family's food budget (two adults, two 11 yr olds, one 6 1/2 yr old, and one 2 1/2 yr old). The parents are overweight and the kids are all in the 80-95%+ range for weight.
I had some thoughts about what you wrote.
To begin, Amanda has a very different situation than yours. She has two very young children and she has the ability to save money on food using "economies of scale". She can buy in bulk and use leftovers to create another meal. If you read closely, you will see she also gets a decent portion of her protein for free (fish).
In reading what you wrote, you currently spend about $600 per month, with an optimal spending of $700. That works out to $20 to $23 per day.
Before prices went up, I had used a baseline cost per day of $8 per person when working with families. That assumes no eating out. The government uses the same basic figures for their "moderate" eating plan. With the increases in food costs, I am now using a figure of $10 per day per person.
As an experiment, I have been tracking my exact spending since the middle of June. I have a jar that I put every receipt in for that calendar month. I make a receipt from the farmer's market. We basically do not eat out, but if we did, there would have been a receipt and it is in the jar. We are now running a little over $1700 per month, which works out to about $10 per day per person. Our food budget is higher than our rent as well.
It is definitely more difficult when a person has food allergies/ sensitivities/ or aversions. We can't use cow dairy so we buy very expensive goat milk butter and cheese (although we use less to balance out the money).
You mentioned that you are "an extremely active adult male with a high metabolism". That definitely adds to your food expense, as you need more calories than someone else.
I appreciate the details as to how much food you eat each month. I see that you consume 42 pounds of meat and fish per month. That works out to 22.4 ounces of meat per day. That is a lot of meat! You eat 4 dozen eggs per month. That is about one dozen a week, which seems reasonable: 1.6 per day (based on a 30 day month). You go through 4.5 pounds of fruit and vegetables per day which sounds like a lot, but that doesn't count the part you toss, like the skin. You go through 4 pounds of nuts, which is a little over 2 ounces per day. Seems reasonable.
You mention that you cannot tolerate beans and prefer meat and fish as a protein source. You don't eat dairy. Starchy foods are also a source of difficulty.
I would wonder if trying to find some types of grains or carbohydrates that you tolerate and like would help your expenses? Working with an experienced NC here or even a natural chef might open up some options.
Setting that aside, we can work on ways for you to save money immediately using what you already eat. The first idea that comes to mind is your protein budget. Generally people save money in this category by buying in bulk. However, we both know that the stores that are cheap in this category are cheap for a reason: they use meat we would not want to eat. Whole Foods has been advertising the fact that they will give discounts when you buy a larger quantity at one time. Perhaps they would be willing to do this at the meat counter. If you bought meat in a larger quantity and then froze it, you could save money. Some people buy it and freeze it raw for use later. Others prepare it, like portioning it into a ziplock bag or glass container with marinade, and then freeze it. You could also prepare it and cook it and then freeze it (like with meatballs). Amanda talked about purchasing chickens on sale for future use, which is one way she saved money.
Nuts are another item you could buy in bulk, if you aren't already. If you buy at the farmer's market, you could ask for a discount if you bought several pounds at once.
One way that many people here save money on their produce is buy buying frequently (to avoid spoilage) and by going "beyond organic", as Amanda says. Getting to know your growers at your farmer's market will let you know who to buy from. Maybe a grower is not "certified" organic, but maybe their practices fall within your comfort zone. They may have decided not to pursue the formal designation, as it is very expensive to do so. A good book on this subject is "To Buy or Not To Buy Organic" by Cindy Burke (2007). This book includes a discussion of the above plus an actual guide to help us with our decisions.
So, that is my way more than 2 cents.

I hope some suggestions are helpful and that this discussion inspires you. I have been greatly inspired by this topic here at Bauman and thank you for bringing up this very interesting "case study".