We are moving in October (late for zone 3!) and I have to move a bunch of trees (small & young), bushes and perennials. How am I going to do this efficiently and is it too late mid of October? Also, I might have access in spring to retrieve some more plants but most likely not late enough to know what's what and where. How do I best flag what I can't take in fall?

Simone: 

The trees can be dug as soon as the fall frosts kill the leaves. Dig them then, and store them with the roots buried  in a pile of sand, dirt, or compost until the new place is available for planting. If the ground is already frozen by the time you get to your new place, store them similarly until spring. Perennials can be treated the same. You wouldn't necessarily have to wait for frost to kill the leaves.