The accuracy of the report is not always conclusive on the extent of the damage, but if the report states deficiencies, we seem to always find deficiencies. A good rule of thumb is to note that while moisture readings are not an exact science and can vary, deficiencies and damages noted are most often accurate.
The existing stucco would need to be removed (to make room for the counter flashing and EZ Bead) and then patched back in afterward. The results will look uneven and obvious. Trying to retrofit weep screed into the system will also not be worth it, as there needs to be a drain plane system in place to connect with the weep screed, without this drain plane system the weep screed is of no value.