Fellow JRT (cross) owner here. How long have you had yours?
Top tips 1-5 would be: Exercise. Exercise. Exercise. More Exercise. And a bit more exercise after that. Minimum of two hours a day, sometimes more like three, mostly off lead. Anything less and I live to regret it - but you already seem to be on that!
If the barking is causing issues, consider covering up the windows e.g. net curtains or there is stick on frosting stuff you can get for window frames. She's probably worried about the things she can see, and so reducing what she can see will reduce the worries and hence the barking. Right now, what she's learned is that if she barks the scary people passing the window keep walking (she's not to know that that would have happened anyway!) so it's what's called a self-reinforcing behaviour.
Kongs are great, but there's a whole world of different options out there. Nina Ottosson toys, for instance, are brilliant, and Kong has a variety of other food puzzle toys (e.g. wobbler, gyro) that DDog loves. This is a great facebook group for ideas www.facebook.com/groups/canineenrichment including DIY options like snuffle mats.
If you want low-stress walks where she can be off lead and not have to meet other dogs, consider hiring a secure dog field from time to time www.dogwalkingfields.co.uk When you say nasty with other dogs - are we talking noisy or bitey? If the latter, please consider muzzling her for everyone's safety - the other dog's, but also hers.
Re confidence, things that seem to have helped my (anxious but full of bravado) dog are
- Adaptil plug in
- Trick training - he's learned some ridiculous tricks because it's a good way to keep him entertained, and because he can be successful (ditto enrichment activities - the easier ones can be great at helping them learn problem solving and confidence).
- Doggy parkour - I've taught him to walk along fallen trees. At first he was quite worried, but he'll now choose to get up and climb them if I so much as look at them. You can do it with park benches and street furniture too - you just need to teach an 'up' command first.
- Avoiding the things that worry him as much as possible - for us, it's changing our routes to minimise the number of motorbikes he sees, through to adding an 'ask before stroking' lead slip because he doesn't appreciate strangers touching him, and will walk away given the choice. You can't avoid everything, but it's about minimising it.
For training, positive reinforcement is the way to go. They'll work for delicious treats, and it's the training method that has been proven to work time and time again. For instance, every time DDog comes back when you call, give her a treat.
I notice you made a passing reference to dominance. Just to let you know, dominance / pack leadership / alpha dog theory has been thoroughly debunked - your dog is not trying to take over the world (or even your house). It was based on some very poorly designed research with wolves (separated from dogs by 10,000 years of evolution alongside humans...), and even the original researcher has now said he wishes he'd never published it. It's also commonly associated with some really dodgy training methods; Cesar Millan is considered a pariah in the dog training world, and for good reason. I absolutely do give my dog guidance and mentoring to make the right choices, but I don't think we're locked in a power struggle for pack leadership.
Don't use punishments or corrections - they're a good way to damage the bond you have with your dog, and don't address the underlying reasons for the behaviour. As an example, if you punished the dog for barking - which she's probably doing because she's worried, she may end up barking less, but it's probably because she's too scared to bark - and that's will come back to haunt you! If you were scared of spiders and screamed when you saw them, and your DP punished you every time you screamed, you would still be scared of spiders. You might also become too scared to scream - and it wouldn't improve your relationship with DP either. Environmental management (e.g. stopping the dog seeing people passing the windows) and positive reinforcement (e.g. treats for not barking) are the way to go.
It sounds like you haven't had a great experience with trainers in the past - are you looking to find another one?
I fear I have rambled a bit 
Terriers are funny things - DDog is my first dog as an adult, and my first terrier (had toy breeds as a child), and my first experience of taking on a dog with issues... it has been a steep learning curve, but an enormously rewarding one. He's almost unrecognisable from the dog he was a year ago.