I did food combining for a few years. I decided that (for me at least) it only applies to certain things. Or isn't that important.
I definitely always eat fruit on an empty stomach. Particularly melons. I'm strict with the fruit thing. I will eat pineapple or papaya or sometimes apple with other food since they have the enzymes that help digest the other food, but in practice that doesn't happen very often.
I find it isn't good to eat a big hunk of meat with a big serving of carbohydrate. Like a steak and baked potato or bread. So if I eat a nice big juicy steak I try to just eat green vegetables with it. Or if I am eating a bunch of carbs like fresh bread, casseroles or dessert, I usually focus on them and avoid the meat. However, that is mainly for large servings of animal flesh. I usually only eat smaller servings. And I rarely eat bread or potatoes, so this doesn't come up much. I do, like you, eat Ezekiel bread sometimes.
I am fine with eating an "egg in a hole" which is Ezekiel bread with the center cut out, with an egg fried into the middle, also using butter. So I've got protein, fat, and Ezekiel bread together and that doesn't make me sleepy or anything, no problems. Another meal that is, admittedly, weird, but does really well for me is cooked oatmeal with a dash of salt, with coconut oil and a raw egg stirred into it, topped with a head of steamed broccoli. There you have carb, fat, protein, and green vegetable. Besides the fact that I think this tastes GREAT, I actually started eating this because I feel very good and "even" after eating it. It doesn't digest too quickly, nor does it make me feel heavy or tired. Recently discovered that as a lunch or dinner item, it goes great with homemade fermented kimchi, which adds the raw vegetable loads of enzymes aspect.
I've decided that fat actually goes better WITH protein and WITH carbohydrates, I try to eat a fairly good portion of good fat at every meal. It helps us absorb things in our food.
So I guess you could so I have thrown the majority of food combining out the window. But I did keep some of it. I just go by how I feel and the nutrition value of the food. I do eat rice and beans or corn tortilla and beans (like chalupas) sometimes and I feel somewhat heavy and tired afterward, I don't know if it is the combination or just too much carbs. Or maybe it is the way that they are made. I've decided to let vegetables be my primary carbs, with small amounts of whole grains on the side, and fruit for breakfast. On the other hand, for example I recently made a big pot of vegan gumbo, for which I soaked brown rice for 24 hours, and soaked and sprouted black-eyed peas. The rest was a lot of onions, celery, bell pepper, tons of okra, canned tomatoes, herbs and spices. When I ate it I would stir in a tablespoon or so of coconut oil. I ate that for several meals and felt fine each time. So maybe the fact that it was soaked and sprouted and stewed, and watery, made it digest easily.
My advice: Experiment on yourself to form an opinion.