So with the latest set of bugfixes the most dire and damaging to my creations was actually the fix to personal safes. A personal safe allowed machines that used chests as an overflow prevention to be stacked closer together (since they don't link and store 2x as much). This allowed my machines to go from 17 long to a mere 10 in some areas. It was a grave boost to miniaturization.
However the bug fix keeps BC pipes from putting items into or pulling items out of Personal Safes, because of this all my currently crafted machines are worthless because they cannot move items past the chests (or from the initial chest) anymore..
So here's my suggestion, one of two things:
1) Implement an Iron Chest, that does what a Personal Safe used to except not Personal, just double storage for 1 space, no connect.
or
2) Make it so that Personal Safes can be made not Personal and be able to be pulled from. Either through config or otherwise.