usually it is no good idea to mix up work with A2plus and other workbenches in one file.
Problem 1 here: After cloning, the clone get's an independent (decoupled) placement of its original. If the original is moved, the clone is not. As the A2plus constraints are only operating at the originals, the clones are not moved accordingly.
Problem 2: I tried to follow your hints and moved the pocket in the block depart. When updating the assembly, the sketches in "body def drill" jumped to false positions. For sure some toponaming issue. See here:
It would be better, if you do such a small assembly completey with the PartDesign WB. If you need it later in a bigger assembly, you can import it complete or only single part of it to a main assembly.