I am not an expert, and pretty new to NFP myself, although I have taken the regular NFP class through the Couple to Couple League and also took the postpartum NFP class. I own both Student Guides.
I am in a similar boat in terms of breastfeeding and trying to avoid pregnancy (but for me the need is not as dire), so I understand that you need some "rules" to work with during this time of breastfeeding and fertility signs that are all over the map.
Anyway, I think you would find a book called The Art of Natural Family Planning, PostPartum Student Guide VERY helpful (2nd book down): ccli.org/shop/onlineshopping.php?criteria=category&f_cat=books&ind=1&order_by=name
It is very clear and easy to understand and tells you the rules for avoiding pregnancy during this time. To put it in a major nutshell, the main rule for breastfeeding is the "Mucus Patch Rule" (mucus patch being "one or more days of mucus sensations or characteristics followed by dry/nothing days, without a thermal shift). The Mucus Patch Rule is: Phase I infertility returns* on the evening of the fourth day* (meaning you can have sex;)) of no mucus sensations or characteristics after Peak Day. "Peak Day," in the postpartum time is defined as the last day of a mucus patch or breakthrough bleeding. Phase I infertility means that after that 4th dry day evening, as long as she is still having dry/nothing days, you can have sex every other day, only in the evenings. (This is so that she can tell seminal residue apart from actual mucus on the days in between. Only evenings is because she will have all day long to determine whether she notices any mucus or not.)
It is important to note that if the temperatures begin to rise, the Mucus Patch Rule does NOT apply. Wait for the start of Phase III infertility according to the Sympto-Thermal rule.
That's almost straight out of the book (which I own). Depending on how many mucus days your wife has, you may find that this requires a LOT of abstaining, but if you need to be very careful, you may have to bite the bullet. At least you will have some rules to work with, though.
The exception to all this is if you can determine a Basic Infertile Pattern in her mucus pattern. According to CCL, a BIP is defined by mucus every single day and the SAME kind of mucus every single day for 2 weeks. The key is it has to be unchanging. In that case, you can ignore the mucus and need not abstain. But you can only establish this after observing the same exact mucus for 2 weeks straight. Any change after that (a dry day, a day of wet sensation, etc.) and you go back to the Mucus Patch Rule. Determine Peak Day, then count 1,2,3, 4 dry days and on the evening of the 4th day she is considered infertile and you can have sex that evening.
Hope this helps, or gets you through for the time being. If you need further clarification (I'm not sure if you're familiar with Phases I, II, and III terminology as I learned them from the Couple to Couple League), let me know and I can try to help.
I suggest you definitely order that book asap because I think you will find it addresses a lot of concerns about infant feeding, postpartum bleeding, temps, mucus patches, etc. It has example charts that I found very reassuring as they looked a lot like mine.
I would not worry about your wife's low temps as the production of prolactin from breastfeeding keeps the temps quite low (sometimes off the chart). Everyone always thinks they have some thyroid problem or something ;) but it's totally normal if you're breastfeeding and simply suggestive of suppressed fertility. I highly doubt your wife has pcos, personally, because she has none of the classic symptoms. If your doctor wasn't worried about the cysts, I wouldn't be either, but that's just my opinion.
Sorry this so long. Hope this helps!
Also, you can search for an NFP "teaching couple" near you here : ccli.org/learn/tcsearch.php