Hi there! Sorry for the response delay, it's been a crazy busy weekend.
Ok, as you're daughter is hovering near 12 weeks, she could probably handle 1hr 20 mins to 1hr 30mins of A time. If you choose a time and stick with it you will likely see naps improve in length, HOWEVER I'm afraid you have entered the dreaded short nap phase. It doesn't usually last too long but I found 3 months was the time when both boys went through a phase for about 3-4 weeks where nothing I did made a lick of difference to their nap length. Once a day I would usually get a somewhat decent nap of 1.5hrs but the other two were 30-45 minutes. It drove me nuts with the first boy, with the second I knew what to expect and just kept on trucking.
You could try to do a set 12 hr day. I do 7-7 with the boys because it works for our house. If DS is awake but just hanging out in his crib, I leave him there while I make the bottle, then I go in at 7 or just before. DS1 now knows that the morning routine is: Mommy showers, then gets DS2, then DS1. It can take a month or so for it to all fall into place but if you're consistent, they'll learn what to expect.
With regards to school pick ups. If you're very close to the school, is there another family that could bring your other child home on the mid-day pick up, or whatever day the timing is poorest for you? Is your LO old enough to walk home with an older student who is a neighbour?
I wouldn't worry so much about the amount your LO is taking in. 4-6oz is just fine for this age and it may be that you just don't have a baby with a big appetite. My kids are these skinny little things but they're happy and healthy.