You've made it this far, you can't quit now. Suppose you tell us what you mean when you say "We've been trying so hard to keep up with her training, exercise etc." I suspect you are still doing the same thing and haven't consistently (every day for two or three weeks) made real changes in your management routine or you'd seem more changes. She is still a puppy and it's going to take another year to make her the dog she can be. Do you attend training classes every single week?
My first reaction is that you most likely are not really doing as much as you think you are. What is the schedule like? Is you puppy sleeping in her crate while you have to work and do chores, what is the structure like for managing the puppy?
Why is the older dog whining to be with you? The puppy should either be on a leash and tethered to your waist or purchase a wire ex pen and pen the puppy in a corner of the main living area so the dog has freedom (which he's earned) and the puppy is still with the family but is safe. We currently have an 19 month old Pointer who I use this method with because he's not allowed to torture my older dogs and is still into mischief if bored and un monitored. We keep the stairs gated off so he can't sneak upstairs to have fun getting into things.
If she wakes up at 4:30, ignore her, use foam earplugs and a noise machine and ignore her. I would cover her crate with a sheet so she can't see you. (she sleeps in a crate at night in your room, right?)
If you are being honest with yourself, is she honestly getting an hour of games and training and an hour of aerobic exercise every day? 6 days of the week is what she needs minimum. Put her in the car and take her places she's never been before and train nice leash walking, use her dinner and her treats. Get her out of the house. Mental work is great. Take the older dog too. This kind of thing will wear her out.
We did attend training classes but they are over now. Nothing is starting until after the holidays. Her schedule is - wake up 4:30 am from her crate in the bedroom (we tried to cover her crate with a sheet and she pulls it through the crate and rips it) and we snuggle and the she goes potty. She eats around 5:15 am and then chews on a bully stick or bone while I take a shower and get ready for work. She plays with me and the older dog (supervised of course) until around 6:15 am. She looks out the window and explores the living room until we go out again for a walk before she goes in her crate for the day at 7:15 am. Due to our work schedules she’s crated all day and gets a potty break or goes to daycare 1-3 times a week. We get home at 4:00 pm and she goes out, plays in the yard with a ball, and then plays with the other dog. We also use this time for training sessions. She eats dinner at 5:00 pm and we walk for about 30 mins. She comes in and is gated in the kitchen as I cook dinner, she’s usually watching me or playing with her toys. While we eat she gets a Kong or lickymat. At 6:45 pm have we go into the yard for fetch, or and/or plays with the other dog or us until 9:00 pm, we also do training during this time.
She is on a leash in the house most of the time unless they are playing. We did have an ex-pen that we used but she is too big for it now. The other dog just wants to be next to me.
We take her in the car at least 3 days a week and she has gone to several stores and outside places with us. We take her and the other dog to my parents house and that doesn’t tire her either. We could excersode her more but we don’t have a fenced in yard and I don’t trust her off leash in a park or on a trail.
Thank you for the reply!