How has she done in the past having the run of a bathroom with those pads or newspaper down? How long is she in the crate? I'm still new at this but we don't crate, Gucci gets the whole bathroom area, bed, food, water. It's still got to be boring for him but he does sleep a lot.
Gucci's poop schedule is such that he goes #1 his first time out in the morning then maybe #2 his second time out in the morning. Have you tried, going to bed earlier, waking earlier to start her and your days earlier? Take her for a short walk prior to going to work, putting her in the crate.... I don't know about you but for me, I gotta wake up a bit, have some coffee before I get to the "PAPER WORK".... Maybe it's the same for your girl.

Just a thought...