Hi, Holly. I am still breastfeeding my daughter (11 months old next week), and I agree that you may meet some resistance with your CF team. Of course they want what is best for child, but I also think they aren't comfortable not being in control, and with breastfed babies, you can't measure and put numbers on things like you can with formula.
As far as enzymes are concerned, it is really tough with little ones, because they don't always follow the same pattern. Your daughter might nurse for 30 minutes one time, then lose interest and nurse for only 5 the next. The hardest thing here is figuring out how many enzymes to give her before she eats. One thing you can do is give half of the regular enzymes before she begins nursing, then if she seems to be eating very well, give her the second half when you change sides. Our doctor suggested this approach, and it worked pretty well for us for awhile.
Best wishes on the last couple months of your pregnancy, and any other questions, feel free to ask. I ran into a few sets of different problems, nursing each one of my daughters, but there were always solutions, it was just a matter of talking to enough people to try and figure them out.