Protein is something I think should best be handled by understanding it the same way we've talked about different sources of calcium. I think protein is one food group that people get a pretty good sense of in terms of what works for them. When proteins aren't being properly digested they create all sorts of problems.
My best suggestion is to rotate as much as possible. If chicken doesn't work, try turkey or fish. If scrambled eggs are a problem, try poached. If mozzarella or other soft cheeses don't feel comfortable, add parmesan. The general rule of thumb is that dairy or animal sourced proteins have complete amino acids but if you don't eat much animal protein then remember that grains and legumes have to be combined. Its tough to get enough protein through grains and legumes without finding yourself HEAVY into carb problems at the same time. Nuts and seeds are a great addition but chew them really well.
Which is another point. We all know to chew our food so it doesn't get stuck, but even that may not be enough. The digestive enyzmes in our saliva are so important and really, you can't chew your food enough. For some people, particularly with proteins, supplemental enzymes can be a godsend.
One other important comment I'd like to make is about water. Water is SO important and I'm a proponent of the 8 cups a day rule. BUT! Those of you who drink water with meals, especially just before eating or with food are going to have WAY more difficulty getting your nutrients out of your food simply because you're washing away those digestive enzymes and diluting them at the most critical point. Try to drink your fluids (all fluids not just water) seperately and between meals.