Taking your suggestions from above, we tried to remove those two issues.
If we set our slab thickness to 18" in that same model, and rerun, we no longer get ECR spikes at the columns and equilibrium errors are reduced to just a couple that are not located near the maximum deflection point.
With those two errors/issues worked out, we were left with the following deflection values:
ACI 9.5 Method: 0.4153"
Load History Final Instantaneous: 1.17"
Any other thoughts on what might be causing the large discrepancy?