Sorry for your loss. I recently went threw something very similar. Mine ended up being a very contagious reptile bacteria that he already had when I got him and not knowing. I learned a soft shell is from a lack of D3.
His yellow bumps are completely gone. I bought him a powder supplement he gets twice a day threw a syringe. seen the vet a cpl days ago, he hasn’t lost any weight but hasn’t gained either.
Update on my Perseus. He spent the night at the vets came home with an antibiotic and an antibiotic soak solution. Dr said it definitely was skin bacteria.