There are lots of ways you can go about crate training/house training and there is a lot of advice out there. I can understand how it would be confusing. So lets start with the purpose of doing this training. Ideally, you'll want you dog to only use the bathroom outside of your home. You'd also like to be able to close her in her kennel at night, so that she isn't roaming around tearing things up.
Now, how do we go about this and what are our challenges? A major challenge is that your dog is still a puppy and it hasn't developed the musculature to physically hold it's eliminations. Animals don't evacuate before birth. They have a thick waste called meconium. They evacuate this after they are born and from that point on, they have to work the muscles responsible for preventing them from using the bathroom. So think of it as if you started working out and someone who had been doing it for a long time started giving you a hard time. It's not fair to expect them to hold it for long periods of time, especially for several weeks.
Moving forward under that assumption, we have to determine whether we want to crate training and potting training to be together or separate. I'd opt for separate as there is a lot of frustration involved with potty training and you don't want those feelings to leak over and be associated with the crate. I would advise you to purchase and exercise pen and put the crate inside of it or tie the panels to the edge of the kennel. Put all of that on an easily cleanable surface and put puppy pads in the exercise pen. By doing this, you'll allow her to sleep and have good associations with the kennel and also have a place to go if she absolutely can't hold it.
You asked when the dog wasn't outside and the answer is as rarely as possible. Again, it's building an association. We're going into this with the knowledge that there are absolutely going to be accidents. We just want to limit them. Think of it like a scale. Every time you dog potties in the house, you put a marble on the left scale, every time it goes outside, you put one in the right scale, and when the right scale touches the table, she's potty trained. Something else to keep in mind is that the marbles get lighter as time goes on. By that I mean that whatever she does the most of when she's little is what she'll remember most strongly, so if she goes inside a lot as a puppy, she's more likely going to have accidents as an adult. That's why you want to go out as much as possible, and all the triggers you mentioned are excellent. Those are when the dog is most likely to go to the bathroom, the same as most people need to go when they get up first thing in the morning.
As to how to actually potty train. Basically, you provide as many opportunities to go outside as possible. If you catch her going inside, try to get her outside. Clean all inside messes with a product specifically designed to eliminate the smell, as dogs naturally want to go where they've been before. Don't leave her loose unsupervised in the house. You can put her in the exercise pen when you can't watch her. Most importantly, don't scold her. It does no good and can damage your relationship. At most, if I catch one trying to go inside, I say "no" in a calm voice, and take them outside. If they keep having "accidents" I reduce their roaming space. You may let her have the run of the house and her not have any accidents for a while, then have to reduce her space back to one room, because she starts going in the other room. It's give and take, you can expect a little back sliding from time to time. That's about it.
As for crate training, I think this method benefits it. Everyone says to take crate training slow and shut the door for seconds and build on that, but everyone also says to shut them inside it all night the first night and ignore their whining. This is the best of both worlds. You can slowly build the time the dog is shut in, yet still have a place where she can potty appropriately in an emergency. This will let you completely ignore any whining she does with out it grinding on your nerves or feelings. It's crucial that you don't let your dog out if she's whining and bouncing around, because just like training any other behavior, she'll learn. If she bounces and whines and you let her out, she thinks that's the behavior that gets her out, just the same as she believes sitting gets her a treat. If I go to open the cage and the dog is whining, I'll walk away and come back in 5min. I'll repeat as long as necessary. Giving your dog something calming to do, like chewing a rawhide, versus a squeaky toy, which would wind her up. These kinds of things teach her to want to be in there. A kennel is not a place to lock your dog away, it's a place where she can go that's just hers, like her bedroom. She isn't bothered or harassed there, she can just be in peace. You want to make it the same as you going to bed at night to rest, not like sending a child to time out in their room.
Lastly, for the clinging, you just have to find a way to not feel like a bad person and put her down off of you and ignore her. It might pull at your heart strings and she may whine and bark, but you need to ignore it the same as with the kennel. It's for a long term benefit. She'll knock it off and start becoming more confident eventually. You should also slowly build her confidence by introducing stimulus and letting her become accustomed to it. Don't take her to petsmart the first week. Bring home some junk from the dollar store that she might not be comfortable with, like balloons and other junk. Remember, that just like with potty training, early development sticks, so if you let her do a lot of bad habits because she's a puppy and will grow out of them, then they'll be the most ingrained behavior. I don't expect anything close to perfection, but I do start behaviors and build on them, like sitting before I put food down, letting me go through a door first, not going inside or outside through a door without an invitation, etc... If you start excellent behaviors and build on them, you'll have a really good dog and the inverse is true as well. Good luck.