I stopped using Ivermectin long ago due to its ineffectiveness in treating worms in chickens. I use Safeguard liquid goat wormer, Valbazen cattle/sheep wormer and Pyrantel Pamoate. All three are very safe for treating worms and all three treat the most common worms in poultry and then some.
As far as soft shelled eggs go, ensure they have crushed oyster shell present, free choice. They are still new at laying eggs, give them time for their innards to get used to producing eggs. If after a couple months soft egg shells are still happening, add vitamin D to their feed. Vitamin D helps with calcium absorption for egg production.
Also the coccidioidomycosis may have something to do with the low weight and soft shells.
What treatment did you use for your birds? Standard treatment is Fluconazole.