I don't know if this is possible to do for a map, but I suggest that use Preset, similar to the real Granny, instead of randomized locations. Basically, you just make 5 Presets. In each preset contains each item, each preset having a different location for each item.

For example, in Preset 1, the Hammer could be in the Safe, but in Preset 2, it could be on the Basement workbench.

This would eliminate the fact that not all puzzles get items in them sometimes, as now you just need to be mindful and not forget any puzzle when placing the items around. I understand if it'd be too hard to do this, however.