| Cuttler |
The items you indicated that are modified (CL vs BAB, and spell casting modifier) are replacing the bonus that is part of CMB. But when making an combat manoeuver check, you are actually making an attack roll modified by the CMB and (from CRB) " Add any bonuses you currently have on attack rolls due to spells, feats, and other effects."
so you can summarize it like that:
normally combat manoeuver:
attack roll = CMB + other bonus related to feats, spells, etc
with CMB = Base attack bonus + Strength modifier + special size modifier
so it is normally:
attack roll= Base attack bonus + Strength modifier + special size modifier + other bonus related to feats, spells, etc
with thunderstomp, you replace BAB with CL and Strength bonus with spellcasting stat, so becomes:
attack roll= Caster level+ spellcasting stat modifier + special size modifier + other bonus related to feats, spells, etc