You're not doing anything wrong. She's a puppy - it's what they do. It's hard to maintain their attention and it's hard to get through their excitability. Things will settle down as she gets older.
Keep your training sessions short - maximum of five minutes - and keep them fresh. For now, she's still only motivated by the treat and that's fine. She's just a baby. It will only get worse before it gets better (as she moves into adolescence even the stuff you thought she knew will go out of her head!). That's the time to have extra patience and just keep on reinforcing what she knows.
Oh, and don't make it so hard for her. Training sessions are about exactly that - training. She should be getting a treat 100% of the time during training and only intermittently outside of training. But she should still be getting treats outside of training. It'll keep her guessing. Also, if you are using a clicker, click = treat. ALL the time, 100% of the time. Otherwise it negates the premise behind clicker-training in the first place and she will just get confused.
Don't expect so much so young - the kind of withholding you're doing shouldn't really be happening until she's much older. You should most certainly not be phasing out the treats at this stage. We seem to have this weird concept as humans that we shouldn't be abundantly generous with treats with our dogs. But honestly, why else should they sit, stay, drop, come etc? Just to please us? I don't think so. When they're young and learning they have to be rewarded for everything they do right, every time. It's only when they get older and are no longer puppies and have their commands very well learned that we can expect them to do what we say just because we say it.
When she jumps, or otherwise misbehaves, end the session and leave her by herself, completely (don't look or speak or act as if she's there at all the instant she acts up) and she'll soon learn that jumping around = end of fun and no attention. It'll work, trust me. It just takes time and patience.
And don't be too hard on her - sounds like she's learnt a lot already and she's just being a pup. If you've been going on too long and she's bored, break it up, end the session - give her a rest and a play and a cuddle. Short, intense training sessions are much more effective than longer, more drawn-out ones.