puppy question re. crating, potty training & barking/howling

Since the moment we got her about four weeks ago, my husband and I have kept Ellie (a 16 week old Miniature Schnauzer/Brussels Griffon mix) on a strict schedule of when we wake up, eat and go to bed. I get up at 6:15 (ideally), take her out, feed her and play with her for about thirty minutes. Then my husband gets up and takes her outside while I get ready for work. We kennel her throughout the rest of the morning so that we can both get dressed, but do take her out at least once more before leaving the house. During the day she stays in her kennel for no more than 4 1/2 hours at a time. My husband works a few blocks away so he goes home at noon to take her out and play with her for a bit. One of us is almost always home by 5:15 - 5:30 and we feed her again around 6:00. We play and train for the rest of the evening and put her back in her kennel around 10:00 or later.

All of that being said, Ellie makes it until about 4:30 every morning before she needs to be let out to go to the bathroom. This is great compared to the 2 - 3 times I was having to take her out a couple weeks ago. The problem is sometimes she doesn't (or probably can't) hold it and pees/poops in her kennel before I can get to her to take her out. Since she's been on a 4:30 streak for about a week now I've decided to set an alarm for a little before in hopes that I can catch her before this happens. Does anyone have any other suggestions? Or ways to increase the time period Ellie can hold it? She does not seem to entirely mind going to the bathroom in her kennel which is frustrating because it's not too big for her according to everything I've read. Any help on this would be greatly appreciated.

On a similar note, after taking Ellie out at 4:30 I immediately put her back in her kennel and go back to bed. She lasts about another hour in there before she starts howling/barking/whining. At this point I know for a fact she doesn't have to go to the bathroom because I've just taken her, so she's basically just wanting attention. The problem is we are not willing to give it to her at this time of the morning. Any suggestions on how to teach her to preoccupy herself or insight on what might be distressing her that I may not be seeing? She doesn't have this problem any other time as far as I can tell. We try to ignore her but she is so loud and persistent that it's virtually impossible. It's making for a very exhausted mom and dad.

And lastly, I am very grateful that Ellie is not a yippy dog. She adores people and gets excited easily, but very rarely barks around them. The only time she does make noise is when she wants out of her kennel and when she's playing. I would like to train her not to bark in general though so any insight on that would be great as well.

Sorry for the rambling post, but this is my first dog since childhood and my husband's first dog ever. We are complete dummies in more ways than one so any help would be greatly appreciated. Thank you in advance!