OP I hope you are having a laugh with this one, but just in case you are serious.
You, and your neighbours, have a right to quiet enjoyment of your own properties. The problems start because everyone has different ideas about what this means and nobody thinks they are as bad as next door.
You say that they smoke on the porch, which I'm assuming is at the front of the house, while the boys play unsupervised in the back.
And you are complaining that the smoke is coming in through your windows, including the bedroom where your baby sleeps.
They have every right to smoke on their property, but if they are doing it outside to protect their own children and prevent their own house from smelling smokey they should understand that you feel the same way about your children and your house.
If it's causing you to keep your windows closed all the time even in this hot weather (and if you are not exaggerating the problem) I don't think you were unreasonable to ask them to move further away because it is affecting your quiet enjoyment of your own home. If it was just that you could smell it in the garden I'd say you were being unreasonable but if it's coming in the house and forcing you to keep the windows closed then I think you do have more reason to speak to them about it.
As for the stone throwing, you are not being unreasonable to be concerned but as it was a one off I think you should let it go now. We lived next door to a family whose son would do this constantly. If he was in the garden and had something he could pick up and throw, it came over our fence.
Small stones, bigger rocks, bits of paving slab, toys, shoes, tools, pegs, small plant pots and garden ornaments. Anything he could get over the fence came over the fence. We spoke to his parents and they said they had spoken to him and could do no more. Even when something hit me and cut my shoulder open, they refused to do anything, implied it was my own fault for being in the garden while he was throwing things and accused us of wanting to force their children to stay inside all the time. Their solution was for us to not use the side of our garden closest to their house.
A one off stone being thrown over while the baby was in the garden would have worried me, especially as it was a near miss, but at least it was a one off and even though you didn't like the mother's apology, it hasn't happened again. So whatever she said has worked and hopefully will continue to work. I think you should be happy with that.
The willy waving. Have you considered shouting "willy willy willy" at them?
Sorry 
I'm not subscribing to the boys will be boys thing, but they are little boys and it's amazing how much they pull at their bits. YABU to imply they are some sort of budding sex offenders because at this age it's still fairly normal behaviour. If it were the older boy you might have a reason to complain but even then, I don't think you'd got many people on here agreeing with your take on it, eight is still very young.
Take the advice you have been given. Put up a fence or a trellis with a climbing plant on it, or plant tall shrubbery and trees. Block the view of your garden from the trampoline.
I can understand your DD being wary of them if one of them has hit her in the face, and as a child I was really annoyed by the little girl next door, a year or so younger than me, constantly calling to me when I didn't want to play with her. But again, block the view a bit so they can't see her from the trampoline and hopefully they will stop calling at her when she plays outside.
YABU to complain that the boys are unsupervised while they play. That's one of the perks of having a garden and several children to entertain each other and that's how they chose to have quiet enjoyment of it.