Guides for measurements are frequently extremely limited; most commercial patterns are sized by bust, waist, and hip alone-- perhaps inseam if you're lucky. However, measurements for fitted garments frequently require far more precision, as seen below:
However, this doesn't necessarily solve the problem of measuring a body that doesn't fit societal norms, and as a plus-size sewist, there's a few tricks I've found for measuring:
Bust: The bust measurement should be taken around the fullest part of the chest, usually over the nipple. To ensure an accurate measurement, this should be done on a person who is already wearing whatever bra they intend to wear with the final garment. Take care that the measuring tape remains parallel to the floor around the entire bust; if it's at an angle, the number will be incorrect.
For plus-size or busty people, always take the underbust measurement as well. The overwhelming majority of patterns are drafted for a B or C cup, with some going up to a D cup. This means that these patterns expect a bust measurement that is two to four inches larger than the underbust; if the cup size is larger than these values, the pattern will need adjustment to fit correctly (which I can advise on further, if needed, but is probably beyond the scope of this question).
Waist: Usually, the waist is described as the smallest part of the torso, but as you have noted, this is not always the case in plus-size people. To find the waistline, have the person bend their torso to the side. The point where the body naturally bends (usually just below the bottom of the ribcage) is where the waistline measurement should be taken.
Hip: For the sake of comfort, I would include the lower portion of the belly in the high hip. The low hip should be taken around the widest point of the hips and buttocks. Again, make sure that the measuring tape is parallel to the floor here.
Depending on the distribution of fat tissue, it may also be important to measure the size of the arms and legs, especially the upper arms and thighs. However, these limbs vary more dramatically from person to person, and will depend on your wife's specific weight distribution and musculature. (As an example, due to my exercise habits, I frequently need to check sizing against my calves, because I accumulate fat tissue evenly across my body and enjoy hiking.) She may have some input on this and be able to tell you which parts of clothing frequently do not fit her correctly.