First advice is to make sure there is no medical reason for him not being able to hold his pee so a vet check is in order.
Do you know his history? Have you had him since a puppy?
I think you need to totally go back to basics. Perhaps consider trying a different pee surface (if he is small enough a litter box maybe? or a patch of sod) as she seems to dislike the pee pads. I would try keeping the puppy tethered to you so you can easily catch the start of any mistakes and redirect them to the appropriate place. Here are some good advice to help you out.
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