Welcome! (now your entered into the drawing twice)
I am so sorry about what's happening to your bunny. Obviously what I say cannot supersede an experienced vet's advice,
but I can tell you that my first bunny, Forrest,(he was a baby too) had syphilis, aka: vent disease.
And had similar symptoms, the sores with pus, the scabbing. But it was not so bad that it blocked breathing, but I can see where it could if it spread to inside.
Check your bunny's genitals. I know with Forrest it was on both. Usually it's on both areas because of a bunny's cleaning
They treated him with three injections spread throughout a few weeks.
But before they diagnosed it as syphilis, the same thing happened with my
vet, and he was rabbit savvy too, so after researching, and I found
out about syphilis, I brought it to his attention, and it was like a light bulb
went on, and he agreed that it could be it.
Well, the shots worked and it went away!
So, I have NO idea if that is what is wrong with your bunny, but it would be
worth mentioning to your vet. Please keep us updated as I also would like to know what they come up with, and I wish the best for your bunny.