Suggestion 1: you should consider applying this only to recipes which include iron AND copper plates as ingredients, and then to recipes which include iron- and copper-including intermediate products. A bit of graph discovery would go a long way. Alternatively, do it for the two separately, and have Ferrous, Cuprous, and Mixed waste, each of which can be processed separately for Iron, Copper, and both respectively.

Suggestion 2: don't apply this to liquid-producing recipes (e.g. 1+ liquid product out) or to recipes with mostly liquid inputs, or else Angel's biochem will get CRAZY.

Last suggestion: look at how Angel's mods make themselves compatible with Bob's. The trick is iterating over the recipe definitions and then applying a procedural, conditional change to those recipes based on your inspection of them.