Just on the fly and of course not tested and most probably performance problems:
DELETE FROM MyTable MyTable_Delete
WHERE EXISTS (SELECT MyTable_Cond.ID FROM MyTable MyTable_Cond
WHERE MyTable_Cond.CPT4 = MyTable_Delete.CPT4
AND MyTable_Cond.CPT4Mod = MyTable_Delete.CPT4Mod
AND MyTable_Cond.ItemCharge <> MyTable_Delete.ItemCharge
AND MyTable_Cond.Eff_Date <> MyTable_Delete.Eff_Date)
AND MyTable_Delete.Eff_Date < (SELECT MAX(MyTable_Latest.Eff_Date)
FROM MyTable MyTable_Latest
WHERE MyTable_Latest.CPT4 = MyTable_Delete.CPT4
AND MyTable_Latest.CPT4Mod = MyTable_Delete.CPT4Mod
AND MyTable_Latest.ItemCharge <> MyTable_Delete.ItemCharge
AND MyTable_Latest.Eff_Date <> MyTable_Delete.Eff_Date)