"Only thing that may take away any confidence is my lab that plays a little rough occasionally, but I try to limit this."

Don't limit this, ELIMINATE this.  She is a baby, or was when she met your lab. Your lab has taught her baby mind that "all dogs dominate me" - she doesn't know from this dog to that dog.  Do not have them play together. 

GSD, as well as being tough and brave, are intelligent and sensitive.  I don't mean weak by saying sensitive, I mean sensitive in the way of perception.  I'm sure GSD people know what I mean and maybe can explain it better if you need it.

Also, as GSD puppies grow, they will often pass through a "spooky" adolescent stage - not real weak-tempered spooks, that's a different thing, but a cautious-of-new-things phase.  That they will grow out of, as long as you recognize the normality of that phase and don't come down hard on them and make them lose their confidence.

IMHO the main thing you can do and do immediately, is keep her away from your other dog.  She'll be an adult before you know it, so just be determined that this phase of keeping them apart is short term and you'll get through it.

I'm sure others will chime in with the doggy esteem exercises.  Don't "hate to say it" but good that you recognize and are willing to build up this dog whose genetics you trust.  Good luck!

Haven't seen the puppy, but out of those lines, it could have high suspicion.  Socialization is different things to different people.  I don't want my dogs social with everyone.  I want them to behave and be tolerant. I am the only person of value to my dogs.  I can't expect a dog to protect me, if I inadverdently want it to trust and befriend every Tom, Dick, and Harry.  there should be no boxer sniffing her.  She is insecure.  In that instance, you cannot console her.  Praise what you like, correct (calmly) what you don't like.  If she hackles, tell her "knock it off" and lightly tap down the hackles.  Don't pet her. Don't scold her.

Stop all that obedience.  Free the dog up.  Get it to be obedient, without it knowing it is learning anything.  It is all just a game at this age....nothing serious and not much responsibility on the puppy.  It is just a little puppy.

And, never would I let it play with the lab at a young age.  That puppy should think it walks on water!!

I have a pup who  is almost three months.  He thinks he walks on water.....part genetic, part environmental, part little snotty boy.  I am in control, he just doesn't need to know it, YET!  LOL

Where are you located?  You need someone who knows DDR or czech GSDs, not mals.

Good Luck,
Debbie

I had a gsd once  that was worthless as a watchdog.  She would not bark, no matter what.  Good thing I had a Scottie who was an excellent little watchdog.    The gsd was my last American-line gsd.   She had ROMs all over her pretty pedigree, was the daughter of a Select male (Woodacre's Dakota) and had everything under the sun wrong with her:  extremely dog aggressive, extremely shy of people, extremely sensitive to noise (had to be tranked for July 4th), had pancreatic insufficiency, seizures, was 20" at the shoulder at 4 months (HUGE, 27 1/2") as an adult, "bird of prey eyes," weak, weak, weak pasterns, Malabsorption Syndrome, and a chronic poop-eater.  She did have great hips, though!