Hi – I am also new to this forum. Your thread made me both smile and sigh mya sounds adorable and sweet (no sarcasm there at all) all the issues listed are normal for this breed and very correctable

My sigh is mainly for your poor wife who has an extra toddler to look after on top of your two boys. Having a puppy is very much the same as bringing a new baby into the house and I would have been behind your wife on waiting till your youngest was 2 years as well. Lecture over

First off I would suggest cage training – put the pup in with an item of clothing or towel that has your wife’s scent on it, put a ticking clock under her bed – this can help as mimics human heart beat. Never found radios ever worked with my GSD. Now mya will possibly cry through the night for first few nights (or perhaps a bit longer as she has already learned that barking and creating a fuss generates results )never put puppy in crate for misbehaving she will associate it and hate the cage – not see it as her safe haven as intended. If her crying is a prob with baby – then perhaps wife spending week with her mom might be answer.

GSD are a breed with bonds to one person – this means when ever wife isn’t about she will fret – thus the toilet probs, poss destructive behaviour and disobedience. If you don’t already – be the one to feed her rather than wife – take turns and also get 5 yr old to do this too. Buy a few of her favourite treats – make her sit for you teach her to lie down – reward with treat – distract with toys rather than tell her off when ever poss. GSD are very quick learners and you will quickly find yourself racking your brains to find new things to teach her.

Do not be a softie and ever give in – GSD do not respect this at all – take the line – you do as i command or no treat – if it takes 20 min so be it when they get to the terrible teen yrs - for real bad behaviour (running amuck and refusing to listening etc) I have learnt that shutting them in the garden for 10min (they hate it) excluding her is a real good way and she will quickly learn to behave – never use the cage for correction – just for sleeping at night and when you are not around to keep an eye on.

Lastly soon as she has had her jabs and able – take her puppy training.

You will find with plenty of socialisation and a firm hand she will quickly find her place in your home. The great thing about GSD is they want nothing more than to please you and be loved – they are happy to fit in with the family as a member and make one of the best family dogs you could ever wish for.
Goodluck with mya – love to hear about updates on her progress.