In my own experience phase 1 wasn’t shorter. Hormones are wacky stuff and one menstral cycle doesn’t mean she’s back to her old hormonal situation. But you are probably safe using the Doering rule. Just have her keep an eye on her fluids for any signs of early fertility. Most moms I know had either regular or extra long cycles once menstration started up again, and those who track these things generally said they had short luteal phases. I don’t know anyone who had really short cycles, which is what would happen if one were having short phases 1 and 3. I know that’s all anecdotal, but it’s what I have to offer. No matter how you look at it, the egg is only present and viable for about 24 hours, and sperm can only hide out in an accomodating cervix for about 4 days tops. So even though there may be confusingly fertile looking mucus for an unusually long time, it doesn’t really mean you have more days to get pregnant. It just means it’s harder to figure out which 5 days or so are really it.
The PP body–particularly one that is breastfeeding–has a hard time building up enough of the hormones necessary to pop an egg. Instead of a quickly progressing from the first wave of those hormones (which make the more fertile mucus come in) to the threshhold level that triggers ovulation, you get a slow buildup.
I know it can seem very frustrating, but perhaps the reason why it doesn’t feel like God’s plan is because there are other factors here (not the NFP) that really aren’t God’s plan. For instance, I remember you posting eariler that your wife had to return to work and is pumping milk. Which is understandable and excellent and not a sin, but it’s not God’s plan for the natural control of fertility either. I read an interesting book called Parenting for Primates that compared the childrearing in many primate species, and in every case except human the mothers are in physical contact with their babies all day and night, with short frequent nursings that go on until what would be comparable to ages 3-6 in humans. Also, the diets of the other species tend to be less artifical and body fat percentages lower. Not that I think we should all give up our jobs and eat organic fruit all day while nursing, but it’s interesting to see that in species with menses like our own, babies are spaced by these factors. If your wife lived in a tribal culture in which she worked physically most of the day with her baby tied to her breast and ate what she grew or you hunted then slept with her baby at her breast all night, odds are good that you would have babies at a rate something like one every 3 years, simply because her fertility would stay low.
Also, while she is nursing, she may be less interested in sex. That’s one common effect of the hormone oxytocin, which is produced when breastfeeding. We live in a culture that puts a high value on sex, and shoves it in our faces a lot. It may be that God’s plan is for you and your wife to be content with less frequent sex for now. One thing that tends to happen in other primate species is that females in the phase of life where they have a baby simply don’t go about inviting males to have sex with them. And even in mated species, that seems to be acceptable to the males. Maybe they can handle it easier because monkeys don’t have sexy beer ads on every 5 minutes when they watch a football game. But for a man in our culture, the invitation to look at women sexually is constant. And the universal horror expressed in the media at the thought of a week or two without sex for anyone over 18 (married or not) makes us think that we must be disfunctional if a month of marriage goes by and we only have sex for a few days in a short phase 3.
I see that you are trying very hard to do God’s will, but that already the devil is tempting you to see it all inside out. It’s not that God or the Church is trying to ruin sex for you. It’s the world that wants you thinking about it all the time, even at the wrong times. It’s the world that forces a non-ideal separation of the infant from the breast (which is a major key to child spacing without tons of abstinance). Remember that you were eager for your wife to resume cycling so that you could more reliably apply NFP. Not that I blame you for that, nor do I think you really had a choice about her going back to work, but it’s a compromise. If she can’t stay with the baby and delay fertility that way, then we’ll have to go to plan B: get back on a predictable cycle and use that to abstain periodically. God does the best he can with plan B, but it’s really not His fault that we aren’t on plan A (where temptation is low and oxytocin is high). And as far as I can see it’s not your fault either. I’m not trying to say that. But your frustration comes from the world, not the beautiful knowledge we have of God’s amazing creation of our sexuality and the female cycles of fertility.