Yes, cleaning with a vinegar and water solution will take away the urine smell but if you keep her in the crate for that long she's gonna have to pee whether she smells the old urine or not.
If you guys leave around 7:30 and don't get back until 5 then that's more like 9 hours. That is way too long to expect a 3 month old pup to hold it. If you keep that schedule what you might end up teaching her is that there is no use in holding it at all so she might as well just pee as soon as she feels the need rather than endure all that discomfort.
You don't teach a dog not to eliminate in their crate. You use the dog's natural inclination not to want to eliminate where they eat and sleep to aid you in potty training. But even still, you can only push it as long as their bladder is physically capable of. Each pup is different in how long they can hold it and in how much they are inclined to keep their living area clean.
I suggest coming home at lunchtime or getting a friend or neighbor to let her out at least at mid-day so she can relieve herself outside.
