I'm no expert, but I'd point out in my experience that there's a line of departure for consuming protein or amino acids. Typically for me that line is the marathon or 50k distance, or 5 hours or less. For runs less than 5 hours, I go with just enough carbs/liquids/electrolytes to get the job done. Longer than 5 hours is when I consider the proteins and/or fats.

Why? Because proteins or aminos are more difficult to digest, I feel the GI tract works a little more in order to consume proteins (or fats.) The exercise nutrition experts can explain better than I, but I think its due to the opportunity cost of blood being diverted away from working muscles or skin in order to digest to protein or fats.

As for the original poster's query to strategy, I typically try to start any longer ultra well hydrated and carbed up. Topped off, if you will. Because of the carb-load, I don't need many (if any) calories in the first 60-90 minutes of the run. I need to deplete my stores a little before taking in calories. After the first hour, then I go with about 200 calories per hour and depending on the temperature about 20oz/hour, but that is a subjective number depending if it's warm out.   Not consuming calories too soon is an important point for me.

As for getting sick of certain foods, I carry a variety of the typical products; a flask (5-6 gels worth), a bag of energy blocks, and a tube of Perpetuem chews.  Indeed, there is a science to ultra nutrition, but it's not a linear equation (eg 200 cal/hour, x oz fluids, y fats, z proteins, etc, etc.)  At some point in your event the variables change. Most 100 mile ultras start in the early morning and run through the day. Running intensity is higher earlier in the day, say for the first 50 miles before the pace slows down. Caloric and fluid intake (and thus electrolytes) are typically higher in the daytime than in night. Once the night comes, pace decreases and naturally does fuel, fluid, and electrolyte requirements.   I'd say this is when ultra fueling becomes more of an art than science. It takes a little tuning in to the feedback loop to know what you need. I'd say fluid needs are less at night.

The important thing is to be sure to carry stuff. For some more advanced ultras where the aid stations are hours apart, running out of calories is detrimental. Having a variety of stuff in your pack (the ziplock baggie idea is great - fill it up at aid stations with solid foods) is key to avoid falling below that line of low blood sugar. Keep eating in small amounts.

Real foods are great, too. Some favorites are trail mix, grilled cheese, quesedillas, soup, and boiled potatoes.

Having a grumpy stomach in the long ultra is not all that uncommon. I recommend carrying a few Tums and/or ginger chews if those occasions should arrive. Be prepared for some rough patches.

Lastly, I'll add that we're all an experiment of one. We don't get to the end of long ultra event very often so its hard to know what works. In a couple of my events, I ran the last couple hours on coca-cola alone after going all day with the other stuff. Never trained with it but it worked.

Good luck!

FYI, Sunny Blende is an authority on Ultrarunning nutrition:

http://www.eat4fitness.com/articles.html

On her website she links all her articles published, including many in Ultrarunning Magazine

Great information. 

I have a routine that I generally follow for marathons/50ks but I am going to do something outside of my comfort zone June.  I am going for 50 miles but it starts at 7 pm and obviously goes all night.  I am really only a morning runner so I am worried about what to eat during the day.  I plan on doing some evening trails runs to practice so hopefully I will work out a few kinks but I know every race is unpredictable. 

Any suggestions or do I just do what I normally do?  Thanks!

I get about half my calories (more or less) from Vi Fuel.  Like you said, tends to be less sweet, plus the anti-fatigue properties are really nice for the long races, like 100s.  The other half-ish comes from real food.  Usually stuff that is savory: burritos, potatoes, bacon, soup, broth, beer (really!), brisket, etc, etc.

Some races I can do more gel and less "food" and other races, my stomach is a bit off and food sits better. 

This is all related to 100 milers.  In 50k it's 100% gel (Vi Fuel) and 50 milers is nearly all gel (also Vi Fuel).

My motto is eat early and eat often.  As far as what to eat, I follow the what looks good or what tastes good.  I make sure to eat something every 30-45 minutes.  As far as what I've found that it changes, I loved grilled cheese during my 24 hour race, could not stand it in my 50 mile one.