Having just went through this I will offer a couple of pieces of advice for you and the others can correct it....
Using 2 crates is an excellent idea. Like Mr. Frawley says, I'm not a big fan of having a dog in my bedroom while I sleep. That is my bedroom, not the dogs. Put the dog in the laundry room crate at night when it's time for bed and ignore all the whining. Your dog is going to continue to whine for a while so get used to it, and ignore it.
I work 9 to 5 like both of you and know exactly what you are going through. Like you I came home every day at lunch to let her out. That is fine. I was off for a good portion of the holidays so I paid close attention to how long she could hold it for, it was right at 4 hours. She couldn't hold it any longer than that. So I made sure I was back home at the 4 hour mark and it worked instantly. I put my night crate in the garage pretty close to where I park the car, so immediately after pulling into the garage I had a 2 feet walk to her crate and would let her use the bathroom right next to the garage in the grass. Just keep coming home for lunch. At 12-14 weeks the dog should be able to hold it for a work shift but you'll have to monitor this closely to find out. My GSD can hold it for a full work shift now and then some.
Like they said, when it cries, ignore. You are dealing with separation anxiety (from the dam and the litter) and you are also dealing with crying on the leash when the dog doesn't get its way, ignore this completely. And do not use newspaper or any store bought potty pads, this only teaches, like they said above, that it's ok to use the bathroom in the house. For me and my dog, I wanted to teach her that it's never OK to use the restroom in the house, never, under any circumstances.
And when the dog cannot be attended to, it belongs in the crate, not running free in your laundry room, not at this age anyway, with the crate door CLOSED. I won't go into it, but this will pay off later.
A good option for you, as Alyssa stated, was for you or your wife to take the dog, in the crate, to work, and leave it in the vehicle. Right now, it's winter so it's acceptable. Every couple of hours, go out to the car, give it some water and a potty break, then back in the crate. It will whine, but like I said, get used to the whining. My GSD is 15 weeks old and she still whines when she doesn't get her way, it will go away. I almost started bringing her to work with me but I figured out she could hold it for 4 hours so lunchtime trips home worked for me. I tried it the first day, and she didn't go in the crate, if she had I would have brought her to work with me in the crate. She is a couple days shy of 15 weeks old now and she can hold it easily for 8-9 hours. Those 4-6 weeks before she could were extremely difficult but that's life with a puppy.
If you haven't bought it yet, buy ED's your puppy 8 weeks to 8 months DVD and throw the potty pads in the trash.