Could you use the J-STD-001 for the cleanliness portion.  Can you make your suppliers certify that the cleaning process for both the automated process flux removal and the manual operations can maintain the ionic residues per the standard?  You can then have them supply the rational of how they comply and audit that process and the records that have resulted from the monitoring of the process?  
Was the rework to components that have little or no stand off of the PCB?  If so they should have formulated the process on how they would handle those parts. Were the products hand washed or machine washed?  Maybe you can make some rules for hand soldering in general in which you can specify ionic removal, verification, and determine a common standard by which to judge the products.  

Kat

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