Taking the pup out hourly is a good rule of thumb.

Plus, every time you go out, you can work on two very important obedience commands- Sit at the door going in and out, and the recall to come back inside.

 Quote: carol boche

I would start tethering her to you instead of allowing her to run around the house with a long line. This way, you can watch her every move and if she does try to "go" you are right there to take her outside without her even getting the chance to get started.

The majority of the problem is when she's in her crate. I think the long line is effective for playtime, we are able to catch her in the act every time on the long line. If she was tethered for playtime, she would not be able to fetch, or run around any. This is part of her exercise/social time. I was asking if there would be a benifit to tethering instead of crating for part of the day.

 Quote: carol boche

Are you allowing her access to water in her crate? If so, I would stop this. I am too also wondering what you are feeding and what the feeding schedule is.

Good point about the water. Now that hubby is home during the day, I don't need to worry about her suffering from the heat while we're at work.
We are feeding raw. Somewhat limited selection because of tummy sensitivity issues. We're trying to get the vet to look into the sensitivity issues. She is fed 1.5 lbs in the morning, 1 lb at lunch, and 1.5 lbs in the evening. The evening meal is very late, and she is fine all night after just one potty walk between feeding and bedtime. She gets water every time we go in/out, except the last walk of the night.

 Quote: carol boche

Puppies are usually really easy to get onto a schedule of when they eat and when to take them out.

This one has been very stubborn. When she was little, she couldn't hold a full meal in her tummy without pooping. We developed a morning sechedule of going out every 20 minutes for an hour or until she pooped, then breakfast, poop break halfway through breakfast, and poop break after breakfast. Making for 5 trips in 2 hours before I went to work in the morning, and she could not be left alone in her crate while she ate. But at least it worked... Now that she's older, she needs much less food as a ratio of her stomach size, and is on a more normal potty walk, breakfast, potty walk. I even have a chance to run upstairs and get dressed while she eats.

Husbands are much harder to put on a regular schedule.

 Quote: carol boche

It is really important IMHO to instill a "go potty" command

She has that. She pees very promptly when taken out. She just has very little concept of holding it until we get there. We give her 3 minutes after that to get a chance to do anything else she needs to. Her poop schedule is fairly irregular, but she does usually hold it until she gets a pee break, so we wait and see what else she may need to do after pee.

 Quote: carol boche

Walking briskly, play or running around will help to get the process started quickly.

She does very reliably poo during her scooter runs, even if the rest of the day is unpredictable. My last Dane had to be walked 1/8 of a mile before he would poo. This is not always an option when traveling, so I'd like to maintain Maggie's ability to go in a small area near me given her 3 minutes.

 Quote: carol boche

When you are home and she is crated, does she settle or raise a ruckus wanting to be out with you?

She usually settles. If she raises a ruckus, and we take her out, and she does nothing, she gets put in the other crate far away from where we are for 1 hour, so we don't have to listen to the barking. (You don't want to be in the room when a Great Dane is barking.) We bring her outside again when she is quiet, and depending on schedule/mood we may have playtime or put her in the crate near us.

She does not know how to settle outside the crate. We are working on that, giving her more out of the crate time as she learns more of her manners. She's very good in the kitchen now, as I've been shaping an extended down by tossing her bits of whatever I'm cooking when she's staying down. Otherwise though she needs constant attention when not in the crate.

To be honest, I totally understand better now why most of the breeders/rescues we talked to insisted on a fenced yard. It is very difficult to keep up with her exercise requirements without overdoing the scootering miles. I'd really love to be able to put her in a secure outdoor kennel when we can't give her the attention level she needs.

 Quote: Alyssa Myracle

Plus, every time you go out, you can work on two very important obedience commands- Sit at the door going in and out, and the recall to come back inside.

We don't have a fenced yard, so that is not where we practice the recall. We do practice recalls from a stay inside the house or on lead outside. She is currently up to a 2 minute sit-stay, we're starting with the down-stay now.

Have you considered doing away with the midday meal, and shifting those portions to the morning and evening feedings?

 Quote: Alyssa Myracle

Have you considered doing away with the midday meal, and shifting those portions to the morning and evening feedings?

Not yet, but soon. We are slowly cutting back her volume, she was getting 5 lbs a day during her fast growth period, and still looked ribby. She's filling out now so we're cutting back.

I don't want to cut out the midday meal until her tummy issues are sorted out. Give her as much time as possible to digest her food by streching it out a bit more.

Sometimes tummy issues are the result of too much food.

You know your dog best, though, and you have to go with your gut sometimes.

You could see all her ribs on 5 lbs a day when she was going through her fastest growth period. I'd totally believe it if her growth needs exceeded her stomach's capacity to digest. I think I already told the story about how when she was a baby she needed 3 walks for every meal (before, during, and after). But I didn't want to cut back on her amount until she started filling out more. Now that she's filling out we're cutting back.

But wouldn't that affect her poo schedule more than her pee schedule? It's been a very long time since she had a poo accident, they're mostly pee accidents.

 Quote: Denise Skidmore

We have not had a uralisis done. The fact that she has no problems at night makes me doubt this is an infection or the like.

That's not foolproof at all, I know from experience.

The urinalysis is inexpensive. I'd do it.

This is what I always do when I have an untrained adult or a new dog in the house or a dog who has exhibited a housetraining setback: I back up to Step One, tethering to me, letting the dog out VERY often, and throwing a party for every good potty. Especially when a crate-peeing habit has started, I'd really up the trips outside and I'd even have high-value treats for "good potty" for a while.

I'd do whatever I could to start a new habit.

It's worth a week or two of a lot of effort.

When a dog has to poo, it can effect the bladder as well. (pressure)
Large dogs look ribby sometimes, during that growth awkwardness stage.
Feeding the same, but in two portions rather than 3 will help you get past the lack of schedule, and will help to establish one a lot better.
I would NEVER change to a kibble diet just to get validity from a vet, I'd find another vet. Vets are annoyingly ignorant about nutrition in the first place, so them not taking you seriously is pathetic.
I'd also add some pumpkin to the diet (if you haven't already) to help stabilize. If you already added it, I'd up how much you give.
Tethering the dog rather than allowing free time on leash will help with the potty issues more, as well as helping the dog to accept crate time better. Not using the crate as much will make for an even MORE indignant pup about the crate as time goes on. If she is creating a ruckus in there, make it a point to be "busy" going in and out of the room, not looking at her. Put earplugs in if needed (or an ipod) whatever is necessary to ignore the fact that A dog is barking at you. As soon as there is quiet, take her out to pee.
If she pees in there even with the breaks, don't rush in to clean it up, wait until she is quiet. You can also try covering the crate with a blanket to help her quiet down. I think that lowering the number of feedings will help regulate a LOT. Hopefully this works out for you, it can be a pain to get through but believe me, we have all been down this road at some point!