Full of admiration that you are sticking with it.
Don't worry, you will soon feel the love for your beautiful machine.
Bit of an essay, but best to cover as much as poss. Remeber you don't have to do it all at once (if at all) and that ultimately the type of bike you end up riding and the type of riding you do is a personal choice made for your enjoyment, no one elses. Help, support, encouragement and humour will always be found here.
First and foremost, your bike should fit you, you shouldn't be trying to fit to your bike. So as previosuly advised, get down to your local bike shop,
They will be able to
tell you if your bike frame size is too big or small or ok
Help with a women's specific saddle,
Set your saddle height and position correctly,
If you find that you have shoulder or back discomfort after riding, you may need to look at a suitable handlebar of the correct width for your shoulders. You may also be leaning too far forward, or not far enough forward so the handlebar stem may need replacing. You may be able to fit spacers to your hadlebar so that it sits a bit higher, or you may wish to look at adjustable stems which allow you to vary the height of the handlebar.
Any knee pain is usually down to cleat positioning if you are using road cycling shoes. I suggest getting flat pedals for the time being. Saddle height can also contribute to knee pain.
Getting wider tyres can help if your bike can take them. More rubber on the road and more comfort.
If you have small hands, and are finding it difficult to reach your brake leavers, some makes allow the lever position to be brought nearer the handlebars - again bike shop can advise.
Bike specific clothing can help, but no need to go full neon lycra bandit, just something padded and relatively seemless for your backside, along with cycling gloves/mitts.
A bit of cycle training can help with confidence too.